I think you're going to see a split here in opinions between the folks who have SC as their primary game (or are Capcom haters) , and folks who are Capcom fans first. One group will be heavily for this, the other against it.
Neither opinion in wrong, but I think Malice's idea is best for any non-Capcom community. Also, you don't have to abandon EVO to participate in MLG. VF5 participated in both in 2008-9 timeframe, and neither community had a problem with that (though VF was way too small to matter) If EVO wants to have SC, that's great, and you should support that. However, it's not something that should be relied on. Especially since EVO has a history of hurting some game communities- GG and Smash being the most notable examples.
If your goal is to compete with Capcom games, the only way you can grow the SC community above the SF community is through bigger prize pots and bigger tournies. That's something that you'll never get as long as you're tethered to a tourney circuit which is based around a competitor's game and doesn't fully respect anything outside of Capcom fighters. If you fail at that goal, you've likely still enlarged the community, and there's little risk- as much of the SC community is outside of the Capcom community, which is likely to start declining soon anyways due to a string of poor/mediocre games (either critically or sales).
It is quite possible that if other fighting game series hoist themselves on the Capcom/EVO banner, they could go down with the ship come 2013-14 or so. UMVC3 hasn't sold that well. AE hasn't wowed people all that much. SFvsTK is probably going to get horrible reviews (seriously, game reviewers I've talked to are calling Capcom stupid, and it's quite possible SFvsTK will be a bad game even without the gem issue) You need to build a scene that can last and grow outside of the Capcom scene.
Personally, I support Jaxel's idea 100%. That said, turning this into SC community vs Capcom community is not going to do any good.
One side suggestion- maybe 8WR should partner with a non-EVO major and declare that as SC's "national". The other majors are often much friendlier to non-Capcom games, and many of them would welcome the support/hype/traffic. Final Round and Devastation are probably the most logical choices here. The stronger the other majors are, the better it is for the FGC and individual game scenes as a whole.