The opinions so far are about right--while in the general case you shouldn't, in the normal case you can. However, I'd consider the regex:

s/<(\/?)u>/<!-- $1 u -->
[download]

just so you can reasonably easily find where you nuked things just in case you ended up munching tags you didn't want to. (A good backup of the files wouldn't be out of order either...)

Update:Missing a slash. Fixed.