Phoenix's Power in Japan say ditch it. They even make a kit to do it. (but they also front mount mr2 intercoolers)
I think it depends on your target output. If your aiming really high (phoenix's power have a couple of cust's cars over 500ps - sheez - and sell TVIS deletion kits) then you need to get rid of it, but you also need a set of 272 cams, an aftermarket computer, and a crank to support 9000+ rpm. And your fuel system and intercooler need a change. Then theres the big hairdrier.
After a long think about it when rebuilding my engine (3sgte in MR2), I kept it.
In a GT4 I'd be even more inclined to keep it, unless, as mentioned above, you were going to go crazy.
But I'd make damn certain it was working perfectly.