Here is my take. God knew these people were going to be amputated. He knew they were going to lose a limb. If he didn't want them to he wouldn't have allowed them to lose a limb in the first place.
Why should God heal amputees anyway? Is there some reason he should? Jesus never did, he healed a man with a withered hand but he didn't produce a full new hand just restored the old one. He healed leprosy and blindness and deafness so I suppose he produced working parts where none were. With the deaf man he even allowed him to understand language and words that he had never heard before. Even if God did this it wouldn't make people give their lives to Him. The 9 Lepers didn't even thank him, the children of Israel complained about the food that fell out of the sky every day, the 5000 that were fed didn't stand by Jesus and all follow him they just wanted him to keep providing food.
He didn't heal Mephibosheth who was Jonathan's son in the old testament from being lame, he didn't heal Paul's thorn in the flesh and Paul had great faith.
BTW on your introduction page Matthew 18:19 is about church discipline and not about prayer, you really should read the verses before it and after. I know it's cliche but it's true you really shouldn't take things out of context. There are several verses out of context there and all over this site. I'm assuming you really don't know this. I'm assuming none of you know Greek or Hebrew or have access to it. Here's help http://www.blueletterbible.org/index.cfm
Also Jesus used Metaphors too and you should learn some textual criticism and Apologetics it would help when talking about the bible. I read Atheist authors regularly.
One more thing. from your front page.
No matter how many people pray, no matter how often they pray, no matter how sincere they are, no matter how much they believe, no matter how deserving the amputee, what we know is that prayers do not inspire God to regenerate amputated legs. This happens despite what Jesus promises us in Matthew 21:21, John 14:14, Mark 11:24, etc.
How can you possibly know this? I know you BELIEVE this and it sounds like you BELIEVE it's an absolute fact which I didn't think Atheists held. Anyway I'd like to see your scientific studies that you've done on this with all the faithful Christians you've tested it on.
There are scientific studies right? You didn't just put this statement up there because you BELIEVE IT BY FAITH DID YOU?
I'm not trying to start trouble here. I would just like to have a discussion based on Logic Reason and scientific facts about your conclusions. That is what Atheists are all about right?