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There are definitely problems with this script like the ones you mentioned.

For performance reasons a lot of things in Drupal are denormalized (e.g. count of comments on a node, time of last comment on a node) and doing "fixes" like this don't take those into account. It's also possible for those values to get corrupted when you delete a user. I contributed a patch to 4.7 that fixes the "forum topic disappears when a user who makes a comment is deleted" which "fixes" the problem but doesn't solve the fact that there is still a comment recorded on the node with a false time.

For the "multiple comments on a node all get the same time" that wasn't a problem here because of the relatively small number of nodes with multiple comments (e.g. 1 in my case) but if that were a problem you wanted to solve there are ways around that either using multiple queries or a php script to set the time at successively longer intervals for subsequent comments.