Screw removal in general isn't too bad. Some doctors will have you walking in no time with no real restrictions. Others may have you take it easy for a bit, but probably no crutches or anything like that except maybe as needed for your own comfort. Whether it allows you to not have discomfort with kneeling, though, is a tougher question to answer. I can kneel with little discomfort compared to my non operative knee (neither likes really hard surfaces like gravel/concrete/etc) but the little I had didn't go away with removal of the screws. What got better for me after having those screws out was the sensitivity and the ache I would get after running.
It is surgery and not to be taken lightly, but in general I don't think there is really any harm in taking them out. It may not help, but it probably won't hurt anything either. What did your doctor say?