Couple of ways:
You could change sql statements to be standard SQL syntax. That would make sure it'll work for everybody. MySQL 4 is significantly different from MySQL 3 (kind of like Apache 1.3 -> 2.0), so many hosts have not udpated yet (same with Apache). In the Geeklog documentation
they recommend MySQL 3.23 or 4, so it would be nice for your plugin, as for all plugins, to work with all those versions as well. It would definitely give your plugin more visibility and it could easily be one of those common, almost standard plugins.
So that would be my recommendation. I wouldn't bother trying to check for the version and using different SQL each time, just use the standard syntax that'll work with both.
The other option would be to put in your readme or documentation that MySQL 4.0 is a requirement. That would probably restrict the audience though. Many people don't have control over what's installed on web servers, and plenty folks won't even know how to check it... They'd probably just like to know that if Geeklog works for them then plugins will work too...
I know that's probably not what you wanted to hear as it would require some re-writing and testing... As for me, I can handle it. If you decide against changing it I'll probably just write some shell scripts to deal with deletes, or I'll just have to tweak your code (which I'm trying to avoid though).