1. A system for providing security in a computer having a virtual machine controlled by a hypervisor, the virtual machine having an operating system with an operating system kernel and an operating system protection module that detects modifications to the operating system kernel, the system comprising: a computer processor; and a non-transitory computer-readable storage medium storing computer program modules configured to execute on the computer processor, the computer program modules comprising: a security initialization module for modifying the operating system kernel of the virtual machine to pass execution from the virtual machine to the hypervisor responsive to a system call issued by a process executing within the virtual machine, wherein modifying the operating system kernel comprises: setting a breakpoint in the operating system kernel to cause an interrupt upon the system call being issued by the process and setting an exception bitmap in the virtual machine to pass execution from the virtual machine to the hypervisor responsive to the interrupt; a disabling module for setting a state in the virtual machine to pass control to the hypervisor during execution of the operating system protection module and for altering functioning of the operating system protection module to prevent the operating system protection module from detecting the modification of the operating system kernel; and a security module activated responsive to execution being passed to the hypervisor due to the modification by the security initialization module and for analyzing the process to determine whether the process poses a security threat.