It'll work fine either way. It's good to have a tube of thermal paste handy for if (more likely when) you decide to take off/remount the cooler, so you can apply fresh material after cleaning the old stuff off.
As for the Freezer 7 Pro, while it does a good job cooling the CPU, like most aftermarket coolers, it lacks the stock Intel cooler's secondary cooling function: blowing air down and out in all directions to cool nearby components such as the northbridge and PWM area.
Some MBs are more sensitive to the lack of this secondary cooling than are other; I'd stick with the stock Intel cooler at least initially to avoid mysterious problems arising from e.g. northbridge overheating.