From what I've read (and to a limited level experienced), the Lame MP3 decoder will automatically compensate for the silence that is added at the beginning of the track, as long as the original MP3 was compressed using Lame. I know MC uses Lame for MP3 encoding, but I think it uses it's own code for the decoding (Lame, for one, supports Freeformat MP3s - ones with weird or high bitrates, whereas MC does not). Perhaps in a future iteration of MC we will see some sort of mechanism to compensate for these pauses...
For now, I'm in the process of ripping my entire collection to APE - desktop hard drives are too cheap not to use a lossless format like APE. As long as you have a good sound card and get a perfect rip off of the CD, APEs should be even better than then real thing (CD) since APEs have advanced error correction built in, whereas the error correction on a standard audio CD is basic at best - and read errors (while generally hardly noticeable) are actually quite common.
Once I've got everything as APE, I'll easily be able to convert to 128 kbps or 192 kpbs MP3, Ogg, or whatever new format comes out for my portable player, without ever having to worry about not being able to go back to the original lossless recording. I'm sure there will be a new standard that will come out soon with better compression, no gaps or pauses, and all sorts of other cool bells and whistles...