I think perhaps it is time to convert more of our BTC to MSC. I'd rather have MSC in a rainy day fund than BTC anyway. As you say, giving away BTC attacts people more interested in BTC, and I'd rather the foundation hold MSC than BTC.
Here's my crazy proposal:
1) Keep only the 1000 BTC we've already moved into offline wallets
2) Use the remainder of our BTC to purchase MSC over the next few months on the distributed exchange
3) Pay all future bounties exclusively in MSC
4) Keep half of our MSC money for a rainy day and/or future distributed bounty system
5) If our rainy day fund becomes excessive, we can always vote to lower the ratio later
I realize that this would potentially make all of our existing investors absurdly wealthy, but, well, the stated purpose of the Mastercoin Foundation is to serve the holders of Mastercoins, and I'm having a hard time seeing this course of action as anything but a huge positive for them, as long as we do it transparently and over a long enough period of time that nobody who wants to sell to us is left out.
Also, MSC prices would probably go up to the point where I'd sell 1% and quit my job to work on MSC, which I hope would also be in the best interests of our investors.

This is an interesting idea, and I applaud J.R. for his transparency and for sharing his ideas with all interested parties. I do, however, have some concerns:
1.) If it is perceived that the Mastercoin Foundation is artificially inflating the value of MSC it may discourage people from investing and thus have the opposite effect. This is the danger of unintended consequences: i.e., that people will perceive the price of MSCs as artificial and not reliable. I think it would depend on how the MSCs were purchase by the Mastercoin Foundation - a small amount over a long period may mitigate this perception. (Keep in mind also: companies buy back stock in limited quantities when they perceive that it is undervalued.)
Similarly, people are attracted to MSC because of its development funds -- it is well funded in an established currency, BTC. If you take that away, MSC may be a less attractive investment for some.
2) The Mastercoin Foundation already has (or will have) a massive amount of MSCs vesting over the next few years. Selling the majority of BTCs for MSCs makes absolutely no sense from a risk management standpoint. The Mastercoin Foundation has massive exposure to MSCs already.
3) If anything, the Mastercoin Foundation should be taking measures to control for the volatility of BTCs by, for example, proposing bounties such as BTCs or MSCs worth at least $50,000 USD. Or by announcing hybrid bounties: part USD/BTC/MSCs. Or by some other means. Whatever it is it should mitigate the risk of over or underpayment to the developers for work done.