Insurance works poorly if you can just purchase it after you get sick. Prohibiting insurance companies from exempting pre-existing conditions means that someone could purchase a policy after getting a cancer diagnosis. The mandate was meant to compel more people to buy insurance to mtitigate that impact. By getting rid of the mandate, they are destabalizing the market. If people can't find policies, or if those policies are really expensive because insurance companies are pricing in pre-existing conditions, then the public will be frustrated with the ACA and support Republican efforts to repeal it.
In other words, getting rid of the mandate is a way to torpedo the ACA, without saying you are trying to remove the popular pre-existing condition portion.
Edit: Also, the mandate itself is unpopular. People don't like being forced to pay for things. So it is more politically expedient to attack this, knowing it will destabilize the market, than it is to attack the ACA head-on.