Yes Ryna, I would echo what Lucia says, and as an occasional meat eater (dare I admit that), I also offer this advice:
* Give up cow. This is not the place to eat beef, even though many venues and grocers offer it. In addition to the religious taboo, the storage and origins of beef here is highly questionable, and not worth the risk. Much of the beef here is actually buff, a different animal, and buff is flat out risky.
* For chicken, Nina & Hagers is the only folks I would trust, and frozen poultry can be found at many grocers around town, as well as at their retail outlet across from the US Embassy. Purchasing there is prefered, as refrigeration at local shops is also questionable, and the constant refreezing of meat can also be a health hazard. This applies to all imported meats as well...
* Wild fish? Ha, well there is Ratna Lake and the rivers if you have a line and hook. There is however, one vendor in town that sells farmed trout that I hear is pretty good, and if you go to the Farmers Markets at either 1905 (Sat) or Yellow House (Sun) you can find that, along with organic hams and cheeses. The ham guy is trustworthy, and sells a safe product. The Cheese lady from Pokhara also sells at these venues, and that's also very good.
Well, best of luck with animal proteins in Nepal - it's a grim situation outside of the vendors that I mentioned.