Mandalorians are always seeking a challenge; turns out the Jedi are considered more of a challenge than the Sith.
It's like Mandalore the Vindicated said "we'd best return to winning the Sith's wars for them", or something like that. I would have preferred then to be a third, independent faction. The smugglers as well.
But they do side with the Republic as well. They sided with the Republic during Kotor II, the New Sith Wars, the Galactic Civil War, the Yuuzhan Vong War, and the Sith-Imperial War.
My guess is they'll eventually switch sides. After all, letting the Sith Emperor consume all life in the galaxy isn't exactly in their best interest.