Literally the day after Mary Jane finds out this information about Gwen and Norman's relationship - both of them are dead (well, Norman wasn't, but no one knew that for years), and Peter is, as MJ stated, "half-mad with grief." Harry is totally messed up and in light of his father's "death," needs his friends, including Peter, more than ever. It served NO CONCEIVABLE GOOD PURPOSE to tell Peter the truth at this time. Again, you have the situation where the principals in the relationship were both believed to be dead, and you have the emotionally fragile son of one of the principals just barely hanging onto his sanity. And as Mary Jane's and Peter's relationship became more serious, MJ could very well have believed that if she disclosed this information to Peter, he would interpret it as her trying to make herself look better by denigrating Gwen’s character. And when Harry was first released from institutionalization in Amazing Spider-Man #151, there was no point in potentially poisoning their friendship with Harry by disclosing his father's indiscretion. MJ may very well have believed that in Norman’s absence, Peter would resent Harry and take out his anger and frustration at the situation on him.
O.K. - so what about after Harry died - and there was no sense in protecting him any more or worrying about his and Peter’s friendship? Well, right after Harry's death, you had Peter's parents apparently returning from the dead, Maximum Carnage, the Clone Saga, and the apparent death of their own child. What time would have been a good time to reveal Gwen's tryst with Norman to Peter? Over breakfast one morning – “oh by the way, Gwen slept with Norman and had two kids.” When Norman resurfaced with a flourish in Spectacular Spider-Man #250 and tormented Peter a little, Spider-Man burst into Norman's townhouse and savagely beat him, all in front of Norman's security cameras. So does MJ tell him "oh, by the way Peter, Norman also fathered two children by Gwen." Frankly, she might have been afraid that Peter would have truly killed Norman Osborn after finding this out. And then it would all have been over. Peter and Spider-Man, as well as her own life, would have been finished. Of course, wouldn’t she have figured that Peter would rather find this out from her, as opposed to Norman Osborn dropping it on him by surprise? Perhaps she should have considered this – because she has to know that Peter is going to wonder for a very long time what other secrets Mary Jane may be keeping from him (but as I’ve said before, I actually like this development because it provides genuine tension to the marriage instead of “oh I’m so sick of Peter being Spider-Man,” or the “WE’RE TOO YOUNG!” bullshit we were force fed during the reboot).