Unless, of course, you believe that the decisions of other people donating to charity are correlated with your own. In this case, a decision to donate 100% of your money to SIAI would mean that all those people implementing a decision process sufficiently similar to your own would donate 100% of their money to SIAI. A decision to donate 50% of your money to SIAI and 50% to Charity Option B would imply a similar split for all those people as well.

If there are enough people like this, then the total amount of money involved may be large enough that the linear approximation does not hold. In that case, it seems natural to me to assume that, if both charity options are worthwhile, significantly increasing the successfulness of both charities is more important than increasing SIAI's successfulness even more significantly. Thus, you would donate 50%/50%.

Overall, the argument you link to seems to me to parallel (though inexactly) the argument that voting is pointless considering how unlikely your vote is to swing the outcome.