The Elric brothers are able to decipher the plan of Father only due to them not being killed. Thus, all Father had to do was to capture and sedate them and leave them imprisoned. This way, both brothers would not cause trouble until Promised Day.
I think this was the simplest solution, isn't it?
Father simply didn't consider them a threat. Like all the homunculi, he looked down on humans, saw them as, at most, resources and overall useless. We get this exchange the first time Ed and Al meet Father with Ling after Father healed the Elrics:
Ling: I don't like him. I can tell he looks down on humans and calls us fools.
Father: When you notice an insect on the ground do you stop to consider it a fool? The life of an insect is so beneath you that it would be a waste of your time to even consider judging it. That would be an accurate summation on my feelings towards you humans.
Why bother going through the effort of chaining up something that can't possibly hurt you? Why even consider such effort? You have a number of incredibly powerful homunculi who could subdue the Elrics at any time, not to mention the power to shut off their alchemy and reduce them to nothing. As far as Father is concerned, why bother?
On top of that, it's probably harder to keep them alive in captivity than to let them run free and hold their friends hostage. The brothers could decide to kill themselves if they felt they had no reason to live. They might be motivated to do so if they thought it might save the people of Amestris.
So if you believe that the Elrics are incapable of thwarting your plans and keeping them captive and alive might be more trouble than it is worth, why bother?
