So there is already an irregularity in the cycle (lemming shortage), but you say this happens regularly, so is probably not an irregularity at all, just part of a larger cycle.
Having said that, a few mice for a few photos won't develop a dependancy in the owls, so no harm done.

But I think the moral question you're asking is whether or not you should be sacrificing living creatures for the sake of a photo. Humans have a funny attitude to life and death, don't they? On the one hand we are taught that all life is sacred, and on the other we see life wasted everywhere constantly, by man, nature, and apparently by God Himself. It would seem that there is nothing more expendable than life.
I'd say if you feel uncomfortable throwing a mouse, don't, but if you do, then throw it.