It seems you have different versions of mysql-server being offered by different repos. I'm not sure which one you had running, so I can't tell you which repos to diable. I'm assuming you are running CentOS, but it could be anything with yum.
You can also use
repoquery (installed with
yum-utils) to check which files your mysql-server package installed and where the databases were located (or find out the initialization script, if that's the way your package installs MySQL).
The next thing, before you do anything else, is to back-up the database files themselves. If you want to have hope of recovering the data, you'll need them.
Once you found out what the exact version of MySQL you were running, installing a fresh box (Amazon's EC2 is your friend) with that exact version and copying the data files over the freshly installed ones may (big if here, and don't do it with MySQL up) allow you do run
mysqldump on your database.
As for you original question, I don't think a sane
mysql-server package would destroy your installed databases, but I wont bet your data on that.