I don't have an issue with it. Really, the slavery issue was one where virtually any decision would have looked bad on paper. Almost any decision in favor of slavery would have increased the spread of a frankly rotten concept and the exploitation of human beings, while almost any decision that tried to restrict slavery would have led to the slave states getting more and more pissy about the supposed interference of their rights. Which, incidentally, is exactly what DID happen.
The three-fifths compromise is one of many times where an apparently bad decision had to be made because it was more pragmatic than others. Refusing to recognize the slaves at all for the purpose of votes would have angered the southern states even more, while recognizing them fully would have given the slavers even more power in the government. The compromise kept the argument settled for at least a little while longer.
Choosing something else purely on the basis of "less bad to swallow" would have defeated the purpose of his choice, which is that the pragmatic answer isn't always a nice one. Indeed, I think that the anger at his decision to use the three-fifths compromise as his example proved a very good point about it: it wasn't a good decision, but could his critics have made a better one under the same circumstances as politicians in 1787?