I didn't mean in the original timeline, actually...but it's clear that he IS there in the church and as he says, he's on his guard. He also says that he's going on even w/o Crono & Lucca...So, unless we're led to believe that Frog would have gotten his ass handed to him w/o the aid of Crono & Lucca (c'mon, you've gotta give him more credit than THAT)...I think it's fair to say that Frog would have saved Leene regardless, so that Marle getting Grandfather Paradox'd doesn't make as much sense as Lucca at first believed.
True, the Grandfather paradox doesn't seem to belong. But that doesn't necessitate the Entity either.
What if the change in the timeline had nothing to do with Leene dying, rather with who accompanied Frog? Consider, on the original timeline Guardia Troops would have probably been with him. In the between-Marle/Crono timeline, Frog was alone. In the Post-Crono Timeline, Frog had Crono and Lucca.
Thus, we don't need to suppose the Entity got rid of Marle, just that Marle's existence was dependent on if Frog alone went to save Leene.
I think we can agree that he would have succeeded no matter what. The question is then what would have followed.
In the original timeline, the Guardia Troops would have ensured that Leene got back to the castle (and at least showed her that her husband cared about her to some extent). In the interim timeline, Frog saves the Queen alone and she has no indication that the King gives a flying rat's arse about her (indeed, he can't even tell the difference between her and another woman). And finally, in the last timeline Crono and Lucca have a very good reason for bringing Leene back to the castle.
Thus, in the interim timeline the lack of Guardia-associated individuals is important. When Marle exists, Leene's salvation is connected fairly directly to Guardia. When she doesn't exist, Leene's salvation is not.
We know that Leene and Glenn had a bit of a thing going between them (possibly playing on the old concept of courtly love). In the interim-timeline, Frog and Leene may have eloped together (as she saw the king didn't care about her, but her frog-in-shinning armor noticed that Marle wasn't Leene and risked life and tongue to save her). She still might have children (probably not, though), but not children that would eventually lead to Marle (as in, not Royal decedents).
Now objections might be raised since such a theory has very little evidence in game (almost entirely circumstantial). However, to note, in comparison offers a mundane explanation for an event that would otherwise necessitate direct intervention by the Entity (a being who's actions are generally well beyond human keen).
