The initial transport might be an issue - but they'll only get that trauma once. and it's easier to move smaller ones. Sedated. With regards ot the "waste" - this is all recyclable. Organic things tend to be. Anything unrequired or unsuitable for that facility is likely to be of use to another. It's not about protien:cost - it's the flavours etc. You want it you have to make it happen, IMHO it can be made to happen and the benefits - real food - far outweighs potential costs, which in a post scarcity environment would be best described as "absented" as it's reasonably consequnceless in the measurements.

I have been doing a lot of math on livestock in space. The amount of protein/pound for most livestock animals is ridiculously expensive compared to other, non-standard sources. The amount of methane, CO2, and waste these animals put out simply doesn't justify their existence in space. Also, how would you keep a cow calm for the flight up to the space station? Flying cows panic! For the record, this is coming from someone who loves a good steak.