Too many tags

I’ve got a multisite installation running various related news and local info blogs. I’m using feedwordpress to get the feeds and site-wide tags to aggregate these on the main site.

I’m using WebNinja Autotagging system to tag untagged posts
All the tags and categories get brought over to the new site too, which helps search them.
The problem is, there are many posts getting tags which are not highly related (eg. the date, short words which are not very specific etc.)
On each blog, this is not big deal, but on the main site I’ve got hundreds of tags, most of them pointless.

This came to a head with a server overload. I’ve since improved other site functions to get things running nicely again (set caching up better and changed from wp-spam free to fv antispam) but they said

“Please review the list and disable any plugins not critical to your site.

We have looked into your site and we see this is causing errors in your database taxonomy that is Post Tags this is a known error in word press. It only starts to error because of the amount of Post Tags. “

So, any suggestions on removing tags, limiting very short tags or those only used on 1 or 2 posts (I’m sure WNATS used to have this option) or anything else helpful. Any comments on this “known wordpress problem”?

Thanks heaps

Dallas