Don't worry about the rebuild thing so much, it is something that is recommended actually, if you remove them the seal gets broken and there is the possibility on re-installation that they leak, which is a much bigger hassle to cure afterwards then it is to just rebuild them up-front.
So you didn't get jacked, it was probably just unnecessarily cautious behaviour by the tire place.
As for the re-program, why didn't they do that for you? Even when I just got my tires mounted at tire rack they programmed the TPMS for me.