On a ship with 400+ people they'd have plenty of other science officers to fill the position, albeit they would only be lieutenants. It's a false dilemma. It's like... installing a navigator who is an ensign as your new chief engineer or NuSpock's protectionist approach because a junior science officer is prettier than him.. A very clumsy plot device that could have been handled better.
They certainly should not have been using the transporter but getting the ship ready for launch was a priority so they were taking risks that they would not have ordinarily taken.
What's more curious is why the starbase didn't just use their own transporter to deposit them without actively using the receiving pad?