It is a little ... cruel ... to think about them being separated after all this, but then again some separation is absolutely inevitable. The Doctor's not deceiving himself enough to think that this really is forever. He's just decided it's worth pursuing in the time they have allotted to them. Whether that sends him into a downward spiral or not ... I guess that comes from being an optimist or a pessimist. The whole "it's better to have loved and lost" argument.