Poor baby!! It's so awful when you want to comfort them but they are mad and scared because of pills! I have found an easy solution to the pill deal if the pill is crushable. Crush the pill and mix it in a very small amount of something sticky like jelly. Take that mix and rub it on the front of their leg above the paw. Rub it in pretty good so they can't shake it off. As we all know...they can't stand to be dirty and will promptly lick every last drop off of their leg!! If you can find something they like that is sticky then they will get a treat as well! I try to do it during a rubbing cuddle session. They give you that look, like...did you do that? I have a couple that will run around like bucking broncos trying to shake it off, thats why it has to be sticky. It has worked great here and they don't get mad because they aren't real sure that I did it!!
I hope this helps with your poor baby and I really hope the pills are crushable!!
Good Luck!