I just don't like direct hp penalties. I believe intelligent undead heal when resting from my reading of the SRD, so you have to make an exception for that, etc, etc. If you really can't stand positive levels, how about a Cha penalty, with them destroyed when Cha gets to zero?
Yes, under RAW intelligent undead have "natural" healing as fast as living creatures.
As for the "you have to make an exception for that, etc, etc", that's all covered in the SQ description I offered.
A Charisma penalty introduces some of the "fiddly recalculations" I don't like about the positive level approach, since a lot of the Slayer's abilities have Cha-based DCs.
It also still mean the Slayer is still losing hit points, since it has Unholy Toughness.
So, since neither of us appear to like the other's current proposals, how about we try something different.
The original entry doesn't describe the slayer "wilting away" once it runs out of dragon HD life energy, so how about we use one of the following:
a) It is immediately destroyed if it runs out of Dragon HD, no save.
b) It is destroyed 24 hours (or some other number) after it runs out of Dragon HD.
b) when it runs out of Dragon HD it must immediately save (Will DC 20?) or be destroyed, and if it succeeds it must keep on saving every 24 hours at a +1 DC each time until it feeds or misses a save and is destroyed.
I'm liking the latter two as it offers more drama as the Slayer searches for a dragon to kill with increasing desperation. Of them, c) is my favorite as it's (more complicated

) similar to how a creature dying from lack of air works, which is also a sort of "running out of life" situation.