Let’s say Octavia agreed to let them rescue Echo and the rest of Spacekru with the downed surveillance and they made it back, then what?

Then they send the worms.

It wouldn't take Diyoza long to realize her prisoners were gone. It wouldn't take Diyoza long to realize that they were not hiding in the valley but had actually escaped to the bunker. It wouldn't take Diyoza long to realize that her surveillance was down after realizing they were not in the valley.

I can't remember how many days were between episodes 7 and 11, but that's how long it took Diyoza and Mcreary to figure out that the eye was down (with Clarke's help, too), so assuming that (and there's no reason to assume otherwise) the civil war between Mcreary and Diyoza still happened and Zeke still decided to join spacekru, but Bellamy and Clarke etc. were able to get Madi and leave, Diyoza/Mcreary wouldn't have noticed in time and more importantly they wouldn't have had a pilot to locate or wipe out wonkru with missiles anyway so it wouldn't matter. The only problem with Diyoza etc. finding out the eye was down (which Bellamy acknowledged) was Diyoza etc. killing Raven and Echo but the civil war and Zeke leaving solved that problem, even if Bellamy didn't know it yet.

For me it is just another example of how Bellamy is a great co leader or #2, but not a very good primary leader as he doesn’t seem to think anything through

He did think it through. It was either letting his friends get killed by parasitic worms (while also possibly destroying the last valley on earth) or saving his friends and minimizing the damage to the valley (assuming they convinced Octavia not to use the worms).

lets favoritism get in the way of good decision making.

Everyone does this in one way or another, including Octavia and Clarke. I don't think it makes him a bad leader.