Globals on/off , PHP.ini and .htaccess - Best solution?

Hi, we have a site that is catering to webhosts and programmers, as you can understand these people know computers and programs :-) They are fooling around with the default settings of their accounts and giving us funny results and basically being a PITA, asking them nicely to quit... we are sure just wont work...so we have decided to turn globals off. We are in the process of doing this to around 250 scripts and now we have run into a problem... (we are on a shared host and so dont have access to our php.ini file) we are planning to turn globals off via a .htaccess file...nearly all our php files are in root (/www/) , but we are also running a third party application 1 directory above root (/www/theApplication/) which requires globals on, when we tried to use a htaccess to turn off globals in the root all sub directories too went off...so we added another .htaccess in the sub and we got errors.... What to do? how can we have globals off everywhere but in the /www/theApplication/ Cheers, -Ryan