Bits and pieces:
The main problem for the people of that planet was that the usual deflector operator died without instructing his replacement in the operation of the deflector.
And Kirk and Spock should realize that this will
happen again. It's a very probable failure mode in a system that is absolutely dependent on this failure never taking place.
Besides, the heroes knew nothing about this when they launched on their fool's errand.
Some would say that treating something of importance like the Prime Directive as an absolute rule is a bad idea.
And others might say that the PD is such a complex system of regulations that even when taken absolutely, it hinges on careful consideration, cross-referencing and establishing of relevant parameters and variables. You start with the default position of no interference whatsoever, and then work from that
towards the solution that will add interference as prescribed.
A computer might go through the parameters and spit out the solution that Picard must follow. But Starfleet probably believes Picard can do the job more or less equally well, and it feels better to have a man in the loop, so the computerized approach is shunned.
After the fact, the civilization will have worked out new things all on their own - or learned that they will never have to work out anything on their own again, because space aliens are there to do it all for them. The former approach doesn't seem too disadvantageous to me...
how can Riker just dismiss Worf's input so easily.
Why not, if he knows the answer to Worf's question? He's the XO - he is at the center of things, receiving more, and more varied, reports than the Chief of Security. Surely he would have the authority to declare "this is geology" when the Geology Department tells him so!
He isn't even hurting Worf's feelings. The Klingon is probably more hurt because Riker didn't properly punch him in the face and kick him in the groin while delivering the negative feedback!