It's not necessarily about how they recorded it, but about how they obtained it.
At this point of the investigation (which is preliminary), "we don't agree to be searched" is legally a valid reason to oppose. If the investigation becomes official, it will be led by a judge and then it will be another matter.
The issue is that sources are to be protected, for freedom of press. "We are journalists" is a very valid reason in that regard.
Sources are not to be protected if they are committing criminal offences.
Let's not be fooled here. Mediapart claims they are targeted for political reason but they are conducting a political campaign themselves.
Edwy Plenel (Mediapart's boss) started his career at the French's Revolutionary Communist League's weekly newspaper...
But I agree that it was rather foolish to demand to search their office without a warrant.
If you classify "valid" journalists by their political journey or ideals, you won't have many people left.
Notwithstanding the likely possibility that even a highly partisan journalist can be professional and can know when to put their opinions aside.
An illegal source is still a source - and the fact that something has been illegally captured doesn't change the veracity it exposes - although it taints the receivability of it as a proof, legally speaking - that's a different matter.
Wiretapping without due legal process is also an offence in France, and "but we are journalists" isn't a valid reason.