I do think there is a slight element of self-preservation in the fact that she doesn't want Sir Thomas to know she loves Edmund. She knows he would be upset, but at the same time she thinks she's wrong too. Look how she beat herself up over allowing herself to think of Edmund in a romantic way. She intended to take that knowledge to her grave.

To her he could be nothing under any circumstances; nothing dearer than a friend. Why did such an idea occur to her even enough to be reprobated and forbidden? It ought not to have touched on the confines of her imagination. She would endeavour to be rational

The idea that Fanny could have said the whole truth about the cousins as worded "Your precious Maria..." above is foreign to Fanny's gentle manner and the way she ever felt. While she was aware of her cousins selfishness, she still loved them.
When Maria and Julia left at the end of ch 21
and how much more their tenderhearted cousin, who wandered about the house, and thought of them, and felt for them, with a degree of affectionate regret which they had never done much to deserve!

If you look at the modest and gentle way she tried to warn Edmund (ch. 12)
“If Miss Bertram were not engaged,” said Fanny cautiously, “I could sometimes almost think that he admired her more than Julia.”, it makes sense that she would think that probable non-conviction would make it hard for her to explain unprincipled Henry to Sir Thomas. She goes on to think (as Rachel G quoted) that the only way she could convince him is to betray her cousins and doesn't want to do it for their sake.

What could be worse than the outburst she got for keeping her mouth shut? If she was acting out of fear she would have given him her reason for thinking ill of Mr. Crawford. Then at least he'd know there was a reason behind her dislike, because all she admitted was that he's a nice guy, with a good temper, and she's grateful for what he did for her brother, but no she can't like him.