It's kind of gross that we're apparently reading about the murder of helpless children and going "hm, yes, important organizational lessons here."
It's not clear that life imprisonment would have turned out very well for the Romanovs, given the lives of other political prisoners under the Soviet system; and simply freeing them would allow them to join their family members in Europe, garner support and prepare for an invasion.
"Hey, at least we murdered them somewhat quickly instead of tormenting them in brutal prisons for the rest of their lives!" isn't much a defense either.