Is this a short term antibiotic? Yogurt, if your cat will eat it and the vet says it's ok, should help the gut. Probiotics can help, too.
As to pilling an uncooperative cat, anything that can be added to food is great, but do check with your vet first. Other options include getting it in liquid (no sugar), or having longterm meds compounded as a transdermal gel. Pill pockets work, though they may be too high in carbs for long term use.
I buy pure l-lysine powder from Amazon and sprinkle 1/4 tsp. of it on each of the cat's food. So much easier (and cheaper) than the paste!followed by a slug of lisine paste given by syringe
