Bounties operate as follows:
You cannot start a bounty if you have less than 75 reputation. You cannot make them for more reputation than you have (you can't start a 100 point bounty with 90 reputation but you can start a 50 point bounty)
Reputation cost for bounties is paid immediately, as soon as you start them. Presumably the user had 106 reputation and then created a bounty for 100 (all legitimate so far) at which point their reputation immediately dropped to 6, which was what you saw after they had already paid the cost.
The reputation is lost whether or not you award the bounty (you don't get it back either way). If you don't award it the reputation goes to waste. However, if you don't award it but you have upvoted an answer during the bounty period, that answer will be "auto-awarded" half the bounty value. The other half is wasted (there's a bit more to this situation but you can read about that on meta.SE if you care to)
As a result, most of what you ask about is based on a mistaken premise.
Details about how bounties work are in the help, in the section on Reputation and moderation, there's a subsection on bounties: What is a bounty? How can I start one? (Edit: now that I've added the link, I see that Nick posted the same link in comments earlier)
with possibly more than you care to know about
penguins bounties to be found in the relevant section of the network FAQ: How does the bounty system work?
The only thing that I see in your question that could be an issue is that someone might be induced to answer a self-study question "in full" in order to get the bounty (who might otherwise follow the guidelines).
Given it has not really been much of an issue so far (both bounties and the special treatment of self-study type questions have been around for many years), I don't expect it's going to substantially impact the site any time soon, so I don't think it's necessary to pre-empt anything -- if someone answers more fully than seems appropriate, the usual approach of a polite comment is usually sufficient, and I expect it will continue to be for the near future.
Consequently, I don't see anything we need to do here, at least not yet.