We've been doing this for many many years and none of the horses have suffered for it.
basically, the horses are on the ground for 6 months/off it for six months, feeding them hay thats come off their own fields does them no more harm than puttting them back onto the grazing would anyway, which is how most people running a rotational grazing system would do it, so unless you're resting your horses field for 2years at a time, they're going to be at an increased chance of a worm burden anyway,....at least this way its used as fertiliser and i get a good hay crop. Coupled with a good worming plan i find it works well, results in lower feed bills and healthy horses. So, i wouldn't worry about it too much