I think if they jump the pit, then yeah, they totally can pass a player in a pit.
But I also think that this can be generalized—maybe not on the HQ board, but playing on other boards and tiles… If you have a definite height advantage because you're righting people down below you, their dice are down by one. And … that would apply to monsters too. The DragonStrike boards have a couple such places that kind of rule would apply. Some WHQ tiles have those kinds of terrain depicted on them too.
The rules are not a suicide pact. If it makes sense, and it fits the expectations of people at the table, run with it.
In this case: Pits are considered to be effectively small rooms below the surface of the board. Monsters don't fall into them, can jump right over them, and you're at a disadvantage both attacking and defending from a monster if you're in one. It makes sense they'd be able to jump a pit that had a hero in it.
Logic: Monsters can pass each other, and so can heroes. Presumably in the EU version, the latter's only true if the pass-ee permits, which is obviously why monsters cannot pass heroes. Why would they permit it?

Want to stab elf!

Oh, Bob! You've come back again?

Yes. Let Bob pass?

Hmm…

You wouldn't!

Ohh, I don't know, he seems to miss you rather a lot…

Not miss this time!
Okay, the heroes would not USUALLY let the monsters pass. But what can they do to block the way if they're down in a pit? Obviously, they couldn't really. Or if they could, the pit must not be very deep at all.
<InSpectreRetro> All hail Zargon!!! Morcar only has 1BP.