ISPConfig have fixed full paths to their bins in their code/scripts when they do the scanning of mail so you'd have to replace all occurances of these calls with your ones.
eg.
PHP Code:
/root/ispconfig/isp/conf/antivirus.rc.master
:0fw
| /home/admispconfig/ispconfig/tools/clamav/bin/clamassassin
:0:
* ^X-Virus-Status: Yes
/dev/null
Not sure where else besides freshclam cron daemon are there any other references to it.
I find the distros aren't fast enough on updating their releases because they have to package it up etc.etc.. so I like my tar ball versions as it's immediate, as long as it works :P