Personally, I like the idea. If a bot starts with 6 charges at full health and 
I've already damaged it 50%, I expect it to be easier to hack since it won't 
live as long as my ally. In this scenario, I would expect it to have about 4 or 
5 charges. As matthias said, at 50% health, it should have 25% of the charges 
(rounding up to higher number of charges of course). In fact, I expected this 
on my first playthrough.

While I understand the hesitancy to add something of this caliber, I also think 
that I should bring up a game that has had huge success with this type of 
feature -- Pokemon.

While I understand that it's considerably different than FDRPG, the idea 
remains the same -- you get rewarded for the work you do. In FDRPG I think this 
is even more important than in Pokemon because, as I said a moment ago in this 
comment, the weaker a bot is, the less helpful it will be for you.

We can leave out the "repair the bots" (*That* may get pretty complex, not to 
mention throw off all balance in the game with other combat skills -- "Melee? 
guns? Pfft, just hack everything to create an army of droids!"), but I feel 
damage -> charges correlation is necessary.