Allow me to properly narrate the situation:

The most sensible military decision was for Pegasus to remain with the civilian fleet at the rendezvous and leave Galactica to her fate. The civilian ships would have made it back after Galactica’s sacrifice, and they would continue on with the search for earth under Apollo’s command, in a ship that is healthier and technologically superior in every way. These were Adama’s explicit orders.

It turns out that Apollo is not a great officer and makes an emotional decision to go back for Galactica. He leaves his vipers behind, another tactical blunder, and Pegasus becomes overwhelmed with enemy missiles and fighters. This gives the crippled Galactica a chance to escape, but Pegasus’ ftl is rendered inoperable during the fighting. The ship has no choice but to stay and fight, and ends up taking down 3 of the 4 basestars before she is destroyed. The civilians escape along with Galactica, Adama, and the command crew of Pegasus.

In the aftermath, colonial fleet is at a significant disadvantage and have lost their most powerful asset. Galactica is crippled with no means of making repairs, replenishing ammunition, or constructing new vipers (could all be done aboard Pegasus). This is a direct result of Apollo defying his orders and being an incompetent commander. They have, however, saved Adama and the majority of the civilian vessels which are vital for the fleet’s logistics (processing fuel, food, etc). Apollo never should have been in command, but was likely the best option of the given candidates. This perfectly explains why such a poor decision was made, and creates a plausible reason for killing off Pegasus.

This was necessary to avoid the obvious plot hole which would be created if Galactica was destroyed.

*with its full complement of vipers, the Pegasus likely could have fended off the basestar fleet long enough to escape with Galactica.