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This article indicates that suphp is slow as it makes php run as a cgi. Instead it recommends restrictions using mod_php - http://serverfault.com/questions/279938/should-i-use-suphp-or-mod-php-for-shared-hosting. Along this thread another poster recommends, http://mpm-itk.sesse.net/ which allows vhosts to be run under different uid and gid.
This restricts the php process to specific directories - http://help.godaddy.com/article/1616