Takign her out would cheapen the first three movies and ruin the driving force behind the series besides the cool SFX.
I say make her less whiney but more doubtful in the sequel and let them be ready to take the next step but being afraid of what the future brings. Then let them see what a super-powered alter-ego can do a family (enter Lizard) and have them struggle through a test of staying together when the stakes get hard (Kraven burying Spidey alive?) and at the end allow them to finally be married.
You ask, where to go from there? Well that is a good point. I really only see room for one more great Spider-Man movie. I mean you can make 5 or 6 but the next one needs to put their love to the test and let them come out unphased. After that an adult Peter married works in long term stories but in singular movies? It'll become more about the villains and SFX if there is a 5 and 6.
Personally I think the next movie, much like Spider-Man 2, writes itself and can be very good in the right hands (which I hope is Sam, Alvin, Tobey, Kirsten and Bill Pope). But if you phase out MJ, sure you can renew the series for another three installments but it cheapens the first three and still loses the point of the series, just in a whole more ackward and boring way.