Hmmm... have you tried playing with the compressor settings? I have the same problem, either direct or miked. Nowadays I generally compress the living shit out the bass tracks (sometimes during AND after recording). The tracks lose something in the process, though.
My only other thoughts would be EQ (the extra E string punch could be super-low end that you can cut) or modifying your technique to not hit the E string as hard (easier if you play with your fingers, and nearly impossible in certain genres). And maybe, worst case, use an E string from a lighter set than the rest of the strings (perhaps a "super soft").
Don't take my technique comment wrong-- I once snapped my low E on stage (abruptly ending our set)! However, I blame the clue-impaired sound guy for a too-quiet monitor.
Then he'd blame me for the pathetic, farty bass tone I had that night, for which I blame my pal's Series 10....
I'm very interested in any other ways to accomplish this.... anyone?