For the longest time I was playing all sides, but probably enjoyed the Railroad faction the most.

At one point somehow Desdemona says they can't really help against the Institute, and I should go forward with the Brotherhood.

I do that, but at one point I'm given the task of killing every last one of the RR folks. Seems a bit weird that I was helping them out for so long, only to gun them down.

Is there any way around this?

So far I can't seem to find a way to progress against the Institute without first wiping out the RR.

Side with the Minutemen, not the Brotherhood, and you'll be able to destroy the Institute without hurting the other factions.

There are three ways to go about this

Siding with the Brotherhood, complete up to Mass Fusion then infrom Ingram about it, leaving Tactical Thinking remain incomplete and as long as you don't speak to Kells.

Siding with the Minutemen, simply shoot a named Institute member, then destroying the Institute, leaving all 3 factions alive.

Siding with the RR would obviously leave them alive.

Thanks, but geez, I was hoping there was another way. I'm glitched/blocked with the MM. Relayed them into the Institute, only to have Preston give me a Ghoul radiant quest - right in the middle of this super-important assault.

In order to continue with the Institute assault, I have to speak to Preston for the next step, yet he only "uh-huhs" and does nothing.

Damn.

OK, thx - I may have to backtrack on some saves, but I think at least one is doable given my Minutemen glitch above.

As for siding with the RR, I was actively with them, but as mentioned Desdemona said she could no longer help. I may have gone just one quest too far with the Brotherhood perhaps.

Even if you sided with the MM, the RR and BoS will still want to kill each other. One wants to save the synths, the other wants to destroy them. The conflict is inevitable. Best you can do is avoid talking to the specific NPCs that send you out to do it.