I think the Lord Ruler was more careful a person than that. He wasn't fearless, he made sure no-one could challenge him. Even if this meant getting rid of all those who had Feruchemy, like he did, lest it combined with Allomancy - making someone who had his powers. Furthermore, he gave his creations - Kandra, Koloss and Inquisitors - weaknesses (Also, he never let Inquisitors reach their full potential by limiting the number of spikes they had).
The Lord Ruler was a pretty careful person. Of course, a lot of his creations had been influenced by Ruin, if I recall, inadvertently making him Ruin army.
I like to think the Lord Ruler was, at some point, aware that leaving his Church, and much control of his empire's economy, to beings that Ruin could influence was unwise. However, maybe by the time the first book came around, his conviction was slowly being whittled away, which was why he let the Inquisitors have their way after Vin was found to be the child of the head obligator.