Fwelin 
The MLP sun does not work like ours, and I would honestly not be surprised if all magic could do to it is move it around the planet at a predetermined distance (I am aware that there was an old, old statement by one of the showrunners that their sun is like our own, but that's crazy iffy just based on how much it's properties are contradicted in the show). Even when Twilight was moving the sun and moon with minimal control in TK and BDaD, they never once got closer or farther than normal. Either that, or the sun and moon aren't actually physical objects, but rather magical projections on the sky that generate day and night (which is apparently more than just the lack of day in Equestria).
Rapid changes in the sun's position don't seem to have any negative effects on orbits or gravitational effects, so it doesn't seem to control that, either.
Finally, the sun might not even generate heat; Celestia moving the sun to directly overhead did not come up as a temporary option during The Crystalling, and eternal night in NMM's bad timeline didn't seem to make the area any colder despite being like that for years, so it seems likely that the sun does nothing in Equestria by generate light, with heat generated by some other means.
So, I think it's entirely likely (though not guaranteed) that the bomb is more dangerous even with Celestia having control of the sun.
Rapid changes in the sun's position don't seem to have any negative effects on orbits or gravitational effects, so it doesn't seem to control that, either.
Finally, the sun might not even generate heat; Celestia moving the sun to directly overhead did not come up as a temporary option during The Crystalling, and eternal night in NMM's bad timeline didn't seem to make the area any colder despite being like that for years, so it seems likely that the sun does nothing in Equestria by generate light, with heat generated by some other means.
So, I think it's entirely likely (though not guaranteed) that the bomb is more dangerous even with Celestia having control of the sun.