I feel as though if you are hoping to preserve the specific biological scope of humanity you have some significant roadblocks on the way. Our species was generated in millions of years of shifting genes with selection factors blatant to subtle, and more recently we've stripped as many selection factors out as we can. (For good reason, natural selection is a harsh mistress...)

Malaria etc still is a selecting factor as has been documented but they're greatly reduced. In Dawkin's 'The Ancestor's Tale', he tells the story of the Russian Silver Fox breeding experiment in which wild foxes were selected for tame characteristics, resulting in foxes that behaved like border collies.

He hypothesizes that if humans were subject to a similar non-natural sexual selection, picking for the 'tamest' humans (adult male chimpanzees will kill each other and definitely don't work well with groups, while adolescent chimps can work together in large groups no problem -- this is another suggestion w/ the skeleton and other claims for the whole idea of species right after the human-chimpanzee concestor being pushed toward neoteny in order to work in larger groups.)

The border-collie-foxes ended up having floppy ears, liked being pet, yipped and enjoyed playing with humans. If Dawkins is correct, we're a bunch of domesticated humans in a similar fashion. When you throw a wrench into natural selection like that, things start to go out of whack instantly like the constant birth problems Pugs have, bloat in Bassett hounds to back problems in daschunds. It's difficult to predict -- a part of the naturally selected whole that had one purpose, modified to another, can have all kinds of unexpected repercussions. Anything that can 'loves' to do double or triple duty in the body.

So unless you snapshot the human genome the way it is and keep people from randomly reproducing as they like to do, you don't get to maintain a 'pristine' human condition.

Is it preferable to slowly wreck and junk up your genome and species via a more or less unguided (at least in the center of the curve) process, or attempt to steer it in a humane way without eugenics by genetic engineering even though the consequences could be drastic?

The bottom line is that our species will change no matter what we do. I don't know for sure, but I would prefer thought going into it over neglect and leaving the whole thing up to chaos.