I assume that Midnight got most of her levels from merging with Mystra.
As far as Cyric is concerned, he started out his career pulling an intrigue/scam on all the followers of Bane/Myrkul/Bhaal by continuing to grant them spells. This became even more relevant when Cyric killed the goddess of lies and illusions. After that, there were all of the events of Prince of Lies and Trial of Cyric the Mad.
Kelemvor is a little harder to swallow. After he dies, he's in hiding thanks to Mask until Mask and Jergal's gambit to oust Cyric from the city of the dead. Now, Kelemvor did partake in a little bit of that uprising so I suppose that justifies a few of his levels. Then once he becomes the god of the dead, I suppose he needs to pacify any dissenters. Doesn't help much but makes the idea a little easier to swallow.
Yes, but the other deities have been doing the same for eons, and the difference isn't so big. Lolth, for example, has 60 HD. When you compare everything Lolth must have achieved during all those ages of intrigue and corruption and war, to what Cyric has achieved during the few years he has been a deity... how come the gap between them is of 5 HD only?
Additionally, gods just earn xp in a way that is different from most adventurers as their goals are different, i.e. deities advance by increasing the presence and predominance of their portfolios as opposed to mortals who gain levels by adventuring and defeating enemies (both are overcoming obstacles but in different ways).
That's my two cents.
Even then, beings like Shar and Selune and Corellon and Lolth and Moradin have been doing the same for far longer, but the level gap is small...
I guess @captain yesterday is right, and their class level is attached to their divine rank. Something like this:
Demi-deity - At least 20 HD (like Imhotep).
Lesser deity - At least 30 HD.
Intermediate deity - At least 40 HD.
Greater deity - At least 50 HD (like Kelemvor).