Blog has been cracked, hacked! – deacivating plugins for upgrade.

I have been having problems with my blog for a few weeks now and it turns out that my index.php file has been cracked. My host heartinternet have disabled scripting which means I am unable to access the admin section to deactivate all my plugins before I do a full upgrade to 2.3.1 (i am now on 2.0.?).

Due to my inability to deactivate the plugins, will this interfere with the upgrade process?