Are "compared to" and "with respect to" interchangeable?

No, these do not mean the same thing. "Compared to" draws a direct comparison between one object and another. The proper phrase in the example sentence is "compared to" - the first enzyme has a higher stability than the second one, so it is a direct comparison.

"With respect to" is a synonym for "regarding" or "in the context of". One could say that an enzyme has "high stability with respect to temperature and time", for example, indicating in what context the stability is being discussed. The phrase is not used to draw a comparison between objects, but instead further clarify or describe particular aspects of one object.