Actually, he just needed to stay away from any really powerful Mistborn. Brandon states in the Chapter Thirty-Eight Part III Annotation that . . .
[Pushing or pulling on metals inside of people's bodies] is a matter of degree of power.
He also states that Vin has to draw on the mists to get enough power to do this, but implies that if someone was strong enough Allomantically they could do it themselves. So by allowing the nobility to fight each other every once in a while, he kills off all of the most powerful Allomancers in the Final Empire, thus preventing one of them from ever becoming strong enough to affect metals in another person's body.
And also, just because The Lord Ruler touched upon Preservation's (Or Ruin's for that matter.) power does not mean every action he does is dictated by them. I believe that The Lord Ruler upon entering the Well of Ascension saw exactly how the Deepness worked, (As it was well upon the land when he ascended.) and through it saw Ruin. Being the "moral" man all men believe themselves to be, he figured out how to stop the deepness (Create an environment where Preservation is loose in the world.) And used the power of the Well to do it.
From then on, whatever else The Lord Ruler did, he would be trying to foster a place both where he was dominant and where Preservation was loose, but not because he had to, because he was trying to do the right thing and prevent the Deepness from ever returning.