There are two sides to this argument. Considering GLaDOS is a being of logic, how could Wheatley help her in the protection of Aperture Science and the furthering of their discovery. The answer being: he cannot help them. The second side is morals. Wheatley threatened many years of extremely hard word. So... Instead of incineration, disassembly, smelting back into raw materials, and removing of all his hard/software.