It is as well to have made

21:19 Jul 16, 2012 

I think Martin's answer, for all practical purposes, is correct. However, I think something is missing, because of the word "as" in the original phrase. I don't know the context, but I think he's not just completely happy with a "step" that was totally good. I think it's a bit rueful--maybe, "It's too bad that he reacted that way/doesn't understand yet, but even so, it's JUST AS WELL; this needed to be done, and it's a little rough, but he'll get over it and it will turn out well in the end."