So this has happened to me on several of the sites I've worked on - try to enable a bunch of module, operation times out, sometimes leaving half-installed modules (which can sometimes corrupt the settings, and at the very least screw up the caches).
What would be nice is if module enabling worked like updating, that is via the batch operations api. I think module enabling is the cause of 99% of memory hogging by Drupal and so making it function as a series of requests instead of a single one would allow Drupal to run on a lot of different machines.
Of course, some people might not like this way of doing things, so an on and off switch might be nice. I'd propose this as a module, but I'm not sure you can make these sort of changes without hacking the core.