It was on a heist mission to get the prism, taking a detour and causing a highly visible ruckus that by all rights should be talked about up and down the sword coast seems like a super dumb idea.
Unless this WAS the heist mission.
If the Prism Heist was occuring in Baldur's Gate, then swooping in and taking it before the Gith get their hands on it would be considered worthwhile, despite the problems it that its noteriety would cause.
Firstly, that city is actually confirmed as being Yartar, not Baldur's Gate. That confirmation was from the devs, not the game so I don't blame you for not knowing that.That's...really lame. They go through all the trouble to make Tav have [Baldurian] responses, you are lead many times to think she was tooling around Baldur's Gate, presumptively the city on the loading "press any key to continue" screen as well, when taken up.
If it were Baldur's Gate, then the writing would be even worse because A) why would they need to send a nautiloid to get it given they're already based in the city and B) no one in the city ever talks about the nautiloid, which would be insane given the chaos of the attack.
On the other hand, people running around a quarter mile from the crash site are unconcerned with it, you'd think it would be a bigger deal.
Much of this apes the Tom Cruise War of the Worlds behavior, from tentacles that grab you (here, they slap you and you get poofed War of the Worlds laser style), like tripods gathering up people also for "processing". Too many later wheels within wheels gumming up this cool, clean, if borrowed, intro. It'll always be unfortunate souls from Baldur's Gate in my mind.