Our cat (rehomed as a stray a few years ago, already adult then and neutered male) has so far not used the hay as his toilet - and he spends the best part of the year sleeping on hay bales (either in the polytunnel or when we store them in the goathouse, where he lives and gets fed.
Also sheep become immune to toxo if they are exposed to it one year. I honestly wouldn't worry about it, as long as you get an adult neutered cat.
We kept ours in a goat pen, covered with mesh for a wee while (he also had an injury when he came, which kept getting infected as he kept licking it... so vet bills galore right at the start), and he lives in there now.
Unfortunately you will find that cats do not usually take on adult rats.... he does catch the odd young one, mostly it's voles. So I don't know how much pest control he actually is....