I believe the realisation that Frank was their only/best option has a few reasons to support it.
Firstly, Frank’s bond with Newt was clearly very strong- it seems as though this particular beast has a strong emotional intelligence and, as is revealed in the story, was rescued by Newt from Egypt. The very reason that Newt is travelling through America illegally is to get to Arizona, and to free Frank in his own habitat. This entire backstory shows the strength of the bond between them, and the fact that Frank never tried to escape when possible, and warns him of any impending danger, further proves the fact. Frank is dependable and the two can understand each other in a way that possibly other creatures can’t, or at least, the other animals that Newt does have this bond with aren’t capable of doing what Frank can.
Secondly, Frank can control the weather. The information given earlier (and later) in the film is that the Swooping Evil’s venom has powerful obliviatory properties, and Newt has been experimenting with diluting the fluid to the appropriate amount to create an obliviate potion of sorts. Frank and Newt’s bond enabled them to work together, control the weather (thereby diluting the potion) and successfully obliviating the area.
Thirdly, time is of the essence. Much as the force-field surrounding the disaster site, as well as in Harry Potter’s final fights, it can take multiple, powerful wizards to work toward a common goal, and I suspect it takes an adept skill, as well as strong concentration, to maintain the spell and to not ‘drop the ball’ so to speak. Dealing with people in these situations calls for communication, planning, and as per my next point, trust.
We have a plot twist revealed at the end of the film in which an amount of trust for a character has been lost. Trusting official members of MACUSA is understandably a brand new hot-topic and so, placing their trust in an animal who will take instructions is clearly a preferable option at that exact moment.
All of this is aided by the fact that the group are currently in disaster recovery. Many MACUSA members are repairing the city and dealing with other evolving situations which we aren’t exposed to, such as detaining a powerful villain at the end of the event. This also left the large group of no-majes just outside of the event still snapping photographs and writing notes. Do note too that this is in a time before mobile phones, and as such, the reports would be made before they would all be communicated to the press headquarters. Anyone still outside and at the scene will be detached from who they are intended to report to, and so holding them there to obliviate them would be ideal, but not very subtle or time-sensitive. Allowing for a large, golden, 6-winged beast to billow out from the ground and into the sky would undoubtedly hold the population’s attention long enough for the rain to fall and for the obliviatory properties to activate. Which they do.
Frank really was their best option for that moment- no other beast or wizard we had been exposed to in Fantastic Beasts could have performed what Frank did. Even the Swooping Death itself would have taken too much time, delivered too-strong dosages, and likely would have become distracted by eating the no-majes brains.