Is the control wiring for my boiler reversed?
Yes, this is backwards -- while leaving it as is is mostly fine, swapping it won't hurt either

This is indeed backwards from the conventional way to wire things -- normally, the switching is all done in the R wire, and C is used as the transformer return.  Putting the switching in the C wire, as the installers of your setup did, works, but has the undesirable side effect that grounding out the wiring from the zone valve to the thermostat or boiler control will cause things to turn on, as the C wire is usually grounded at the transformer secondary.   Oops!

Swapping R and C at the transformer won't hurt anything either, though, and probably is a good idea because it's far harder to tell with electronic controls whether they want to be finicky about which wire is which -- older electromechanical controls never gave a toss, which is why it worked just fine for all these years.  (My suspicion is that your new control won't be particularly picky, but I'm not a tech support guy at Tekmar, so I don't have any insider info.)