They can and should've went through with the plan. The Ba'ku needed to be moved in order for the Federation to collect a resource in Federation space. I can guarantee that if the Federation caught wind of a Romulan invasion that was going to cut through Malcorian (First Contact) space, they would make a stand there if it made sense regardless of what the Malcorians think. See Errand of Mercy. Ideally yes. But the good guys are still wise to pay attention to logic, common sense and extraordinary circumstance. If the Prime Directive was a hard and fast rule, it wouldn't have forty-seven subsections. We wouldn't have the Omega Directive. Now for the record (something I've stated before), I don't think Meta-phasic radiation is a game changer for the Federation. My reasons for moving the Ba'ku are more about the long-term survival of the Ba'ku and the likelyhood Starfleet would become involved in a protracted conflict over control of the Briar Patch at some point in the future.