I'm surprised (or rather, I'm unaware of) there is no native MySQL solution for this situation.
Considering it's not a mysql specific problem I'd be surprised if there was.
Postgres lets you do database changes inside a transaction, eg:
begin;
alter table x add column y int;
...
commit;
but two problems with that:
1) mysql doesn't support it (nor do a lot of databases) even when using innodb (and using myisam is out of the question for this because it doesn't support transactions)
2) it won't help in a web environment because you can't rollback once the transaction has finished & you are testing the changes and then find the problem.
No easily solution unfortunately apart from writing 'undo' scripts or having a backup handy..
--
Postgresql & php tutorials
http://www.designmagick.com/