Separating 12-3 wire from panel to feed a bathroom fan and light
You're using the word "wire" to describe what is actually "cable".  12/3 is a cable that contains 3 conductor wires plus a ground wire. This matters here. 

First, find all the other multi-wire branch circuits

OK, this is priority one.  You need to get inside the panel, and search the panel for more circuits like this one.  You stated they are on independent breakers; they need not to be.  

They need to be on 2-pole breakers, which is a double breaker which fits in 2 spaces (or straddles 2 spaces, as in GE Qline and Crouse Hinds).  The most important feature of this breaker is that the two handles will be factory-tied together. 

This is to provide common maintenance shutoff, but it also assures they are on opposite poles of the circuit. That is to say, there must be 240V measured between the two hots.  If there is 0 volts, that will overload the neutral wire.   A classic blunder is to free up space by moving these from a 2-pole to a tandem breaker (note handles not tied). 

Further, anywhere both hots are present, the neutral wire must be pigtailed. That way, any device can be removed without breaking the other half of the circuit.  

Other than that, Mrs. Lincoln, Multi-Wire Branch Circuits are rather wonderful, in my opinion, and a great way to get 2 circuits almost for the price of 1.

Option 1: Cap it off and don't use it

In this case, you simply stop using the red wire.  Cap it off on both ends, stick a wire nut to cap it off, and tape the wire nut on the wire (they tend to fall off when put on a single wire).  

Don't cut it - for one thing, it is hard to insulate a wire that's been cut back to  the sheath, and for another, the next resident may want a heater and wouldn't that spare wire be a nice Christmas present for them!  Or, your wife could get sick of the hair dryer and curler tripping the breaker constantly, and look at that! Spare circuit right up in the ceiling! 

Use the spare half-circuit for something else

You can't have bathroom receptacle loads power anything in any other room.  That restriction does not apply to bathroom hardwired loads.  Since half the circuit only powers bathroom light and fan, you have loads of capacity on the black half-circuit and 100% capacity on the red half-circuit.  You can get 20A out of both of them! 

So add 2 circuits to anything you want.  It could be more kitchen countertop  receps.  It could be 2 bedroom circuits.

Heck, you could bring them both down to the bathroom receptacles and now you have 3 circuits for bathroom receps. That takes care of the curling iron + hair dryer problem!  Honestly, 3 circuits in a bathroom is a little excessive, even for me, so I would then liberate the original recep circuit for something else. 

Do the Harper Shuffle

If routing makes this feasible, I would do a swaperoo.   I would dedicate the MWBC to bathroom receptacles, so you have 2 full circuits for receps. 

Then, I would take the original bathroom receptacle circuit, and use it for lights, fan and room for heater. Because in the modern age with LED lighting, a whole MWBC is overkill for that. A plain 120V/20A circuit has 1920W of provisionable power; a heater takes 1500, a fan takes ~150, and LED lights won't be near 270W. 

And -- this solves the problem of hair dryer overload killing the bathroom lights.  A receptacle overload will most likely trip both half-circuits; but since the lights  are on a totally separate circuit, non-issue. 

If you abandon the MWBC, you could still do the recep.

Suppose you decide to cap off the red wire and just not use it. You still have well in excess of 1500W of usable power on the lighting circuit, that's just being wasted.  You might as well bring that down to a receptacle and let someone use it!  

However, you don't want them overloading that circuit and killing the lights, so I'd arrange it so there's only a single receptacle socket available to them. (plug-in devices are UL-restricted to 1500W).  They make 1-socket plain receptacles, but you'll need GFCI protection for a bathroom recep.  That's a bit harder, but they do make combination GFCI + receptacle + switch devices, with 1 switch and 1 GFCI-protected socket. Perfect, and you can even put the switch to good use! 

Also, once any part of the MWBC has a bathroom recep on it, the other half can't be used for anything outside that bathroom. So this depends on you abandoning the other half of the MWBC (or using it in this bathroom).  

Remember, this is the 2010's oh wait. You need switch neutral.

You mentioned running a single 12/3 down to the switch. Nuh-uh.  Consider the wires that need to be at the switch: 


Always-hot (to supply switches obviously) 
Neutral (as of NEC 2011; to be available for smart switches; however, this also makes it available for the receptacle I mentioned)
Switched-hot/Light: hot when you want the light on
Switched-hot/Fan: hot when you want the fan on


Further, you're up against a different rule, that says Currents must be equal in each cable or conduit. So you can't just use two 12/2 cables.  There are several ways to skin this cat. 


Use one fat cable with enough conductors. They do indeed make 12/4 cable, and even 12/5 cable (to provide future option for the heater or using the other hot).  
Use conduit, and run individual wires as needed; it's what I'd do.  
Run two switch loops. However, due to the 2011 rules, both switch loops will need to use 12/3 cable, so you'd run two 12/3 cables.  Each loop needs its own neutral; you can't shortcut and use a 12/2 for the fan, because if someone installs one of those pushbutton timers that needs neutral, it is not allowed to poach neutral from the switch 12/3 (that would make currents unequal in each cable).  
Extend always-hot power from the fan box, down to the switch box (say, in a 12/2 cable, or a 12/3 if you wanted the option to bring down the other hot, say, for receps).  Then, use a second cable (12/3) to power fan and light, in the usual way.   However, this means you have two different things going on in the ceiling box: extending the supply cable, and supplying the fan and light. These should be separated 100%, i.e. extend the supply, then lay a piece of saran wrap in there to encapsulate that wiring since you won't touch it again, then wire the fan/light normally.  You will need a deep box for this since you'll add a bunch of cubic inches for all that splicing.