They will be fine. I like to prune my clients' trees at least up to 6ft high as it makes things much more practical.
Don't cut into the base of the branch (ie the slight swelling right at the tree trunk). Cut just before this. If the branch is heavy make a cut from underneath first, halfway into the branch. Then make a cut on top, 1 inch further out from the trunk. The branch will snap off without the bark ripping away (which would encourage idsease). Then trim off the stump to the collar as mentioned above.
Any cuts you make will heal if left alone, you don't need to put anything on the open cuts.