Like Gerard, I'm quite confused at the purpose of trying to get people to stop donating to the Wikimedia Foundation, and am a bit disappointed to see such a suggestion coming from someone who holds advanced rights on some of the projects. I also note that the response of CIS-A2K's executive director notes that if it is determined there is a problem in terms of their salary structure, it is one he wants to address, even if it may take some time to do so because he (reasonably, imo) doesn't want to cut the salaries of current employees steeply. Looking at the table, it looks like CIS-A2K's total staff budget is a little shy of $300k a year. The FDC is currently handing out what, $6m USD a year? Even if CIS was entirely funded out of the FDC (and it isn't, their APG request is for less than $300k,) that's pretty much a drop in the bucket of available funds.
It's been made clear that just because CIS may be awarded funds doesn't mean that WMIN won't also be awarded funds, and that the entities aren't in direct competition with each other. Trying to do something like get people to boycott donating to the WMF because CIS is asking for a fraction of a percent of WMF's total budget and something like 5% of available FDC funds to be given to them is pointless if you don't succeed and shooting yourself in the foot if you do succeed. If you were partially successful, your own funding in future years would likely be diminished due to less overall availability of funds, and if you were fully successful... well, Wikipedia wouldn't exist.