This is totally untested, so I don't know whether it will work or not, but make a back-up before you do anything 🙂
I currently have PHP4+ and PHP5+ running concurrently by having seperate httpd.conf files. However, apart from running on different ports, the main difference is where I get Apache to look for the php.ini file.
To this end, I have
LoadModule php4_module c:/php/php-4.3.10-Win32/sapi/php4apache2.dll
PHPIniDir "c:\php\php-4.3.10-Win32"
You could try setting your PHPIniDir in your virtual host setup to the location you want.
Like I said, totally untested, but you never know. Would be interested in finding out how youget on.