It let them have multiple tries, and a chance to steal it undetected.
If Fluffy was killed or injured, it would make it obvious that someone was trying to get to the Philosopher’s Stone. Harry, Ron, and Hermione used Fluffy to figure out if the Stone was still safe and protected - Dumbledore and the rest of the staff could do the same.
“Every time they passed the third-floor corridor, Harry, Ron and Hermione would press their ears to the door to check that Fluffy was still growling inside. Snape was sweeping about in his usual bad temper, which surely meant that the Stone was still safe.”
- Harry Potter and the Philosopher's Stone, Chapter 14, (Norbert the Norwegian Ridgeback)
This wouldn’t be as much of a problem if they successfully stole the Stone, but if they got only part of the way through and then failed to get it, they’d cause Dumbledore to increase the protection. After the break-in at Gringotts, Dumbledore moved the Stone to Hogwarts, and after the failed attempt at Hallowe’en, he added the Mirror of Erised to the Stone’s protection. Continued failed attempts would just make him keep increasing its protection, making it harder to steal it. It’d still be useful if Quirrell and the Dark Lord were able to steal the Stone successfully, since the Hogwarts staff would remain unaware of its absence or the Dark Lord’s return.
In addition, killing Fluffy and the troll might not be that easy.
The Dark Lord was still weak, and Quirrell was being weakened by the Dark Lord possessing him - it might not even have been possible for them to kill Fluffy and the troll in the state they were in. We don’t know much about three-headed dogs, but Hagrid seemed to think taking care of one would be comparable to taking care of a dragon, so they’re probably fairly difficult to handle.
“So I told him, after Fluffy, a dragon would be easy …”
- Harry Potter and the Philosopher's Stone, Chapter 16, (Through the Trapdoor)
Trolls are known to be very strong, very violent, and large.
“The troll is a fearsome creature up to twelve feet tall and weighing over a tonne. Notable for its equally prodigious strength and stupidity, the troll is often violent and unpredictable.”
- Fantastic Beasts and Where to Find Them
Even if it wasn’t a bad strategy to attempt to kill the creatures guarding the Stone, it’s not clear that Quirrell and the Dark Lord would actually be able to successfully kill both of the creatures in their way to the path of the Stone. Neither of them was at their strongest, and magical creatures can be quite difficult to handle, especially as they can be resistant to spells.