In that is fine; in fact, it is formal rather than 'basic'.
Whereby, on the other hand, is impossible here: it means by which, and therefore claims that the fact that de-identification differs from anonymization the means by which the difference you describe comes into being: which makes no sense at all.
The problems with your sentence lie in what follows the subordinator.
Properly, what follows in that should be structured as a statement which tells the reader how de-identification differs from anonymization rather than merely describing the two processes and leaving it to the reader to discern how they are different. Specifically, the subject of the that clause should be de-identification.
Latter and former have no place in contemporary writing. Your use of them here is time-honoured, its logic is impeccable; but in a complicated sentence like this it puts a wholly unnecessary processing burden on the reader, especially when you flip the terms out of their original order. Readers are not computers, and texts are not programs: find a way of expressing your meaning that doesn't make the reader look up the refrences.
Here are couple of ways to avoid these problems:
De-identification differs from anonymization in allowing [or in that it allows] a trusted party to re-identify the data, where anonymization is supposedly irreversible.
The difference between anonymization and de-identification is that anonymization is supposed to be irreversible but de-identification allows a trusted party to re-identify the data.
These are a little bit longer than your sentence, but they're a lot easier to follow.
I have no idea what that supposedly means, so you might want to clean that up, too.