That's actually less of a problem than you make it out to be. KOTOR and KOTOR 2 didn't share a protagonist, nor did they share most of their story. Revan was referenced in KOTOR 2, but he didn't have an impact on the plot, which concerned a bunch of renegade Sith Lords and an exiled Jedi. It helps that the two games were written by totally different developers.
Really, they could make a KOTOR 3 that has zero plot connection to Revan or the Exile, and it would be in keeping with the trends of the series (which was called Knights of the Old Republic, not "The Adventures of Revan") and coherent with the eventual fates of Revan and the Exile as established by the novel tie-in and SWTOR's canon.
Of course, the fanboys would kick up an unbelievable shitstorm if EA released a KOTOR 3 that didn't have Revan or the Exile in it, even if it was in line with the previous two entries. Actually, I don't think EA should release a KOTOR 3, just because it would be impossible for them to look good while doing it. It's such a eulogised property that any changes - any updates to the mechanics, any flaw in the writing, any failure to pay dues to the other entries in the series - would be seen as heresy.
EA's so widely hated at the moment that I don't think any KOTOR title they could produce, no matter how good, would actually translate into a good response from the title's fanbase. And Bioware has been the internet's punching bag ever since DAII and ME3. If I were them I'd focus on keeping SWTOR afloat rather than trying to please the unpleasable.