Is it bad to have a circuit breaker on both ends of a feeder?
The breaker in the main panel is the ruling breaker, as it protects the wiring between panels.  A "main breaker" in the subpanel cannot protect that wiring, so it serves only as a shutoff switch, AFCI or GFCI if equipped. ** Therefore it doesn't matter if the subpanel breaker is larger than the main panel breaker.  There is nothing wrong with this and it is often mandatory. 

If you want a shutoff switch (or master GFCI or AFCI) in the subpanel, select a subpanel which does that, i.e. a "main breaker" panel rather than a "main lug" panel.  Main breakers make affordable shutoff switches. 

Note that such a shutoff switch is mandatory when the subpanel is in a different building.



What if you have a main-lug panel?  Can you just install a regular breaker of usefully large size, and backfeed the breaker?  Not quite.  Anytime you backfeed a breaker, it must be bolted down.  (you can imagine how that rule got written.) You will need to either 


already have a panel type where breakers bolt down (Siemens, QOB, Pushmatic)
bolt down the breaker using a listed method (which presumes the panel provides the right bolt-downs, and a breaker with the right holes/brackets) 
add an external shut-off switch
swap the panel out for a main-breaker panel
or if legal, do without a "main" breaker. 


Edit: Here's an interesting listed method for Siemens snap-in panels to bolt a breaker down. This gen/utility interlock bolts directly to the breakers, and locks them together in a way they can't rotate to snap out -- thus satisfying boltdown.  In your case, you're only after that, so the other breaker position is wasted.  Do not use Siemens breakers on anything but a Siemens panel ***. I hear they'll snap in, but at wrong clamp tension etc.  



** Hypothetically if you provided a 100A feed on #1AL wire to a 60A subpanel, the 100A in the main breaker would protect the wire, and the 60A "main breaker" in the subpanel would protect the subpanel.  But that installation would violate diy.se's advice of "get a really big panel".  Also the 60A wouldn't necessarily trip first.

*** Siemens does make breakers specifically designed to go in a QO panel. (why??) Those are for QO panels only, don't even use them in Siemens panels.