Nah early game the capital ships will have to retreat vs LRM blob. Don't kid yourself man.
There are lots of ways to get around that. My favorite is to jump in a Radiance, order it to fly right up into the LRM blob to literally smack noses with another ship, and then jump in a Progenitor to do shield repairs while basically having it run right into the back of that Radiance. This allows both ships to have all gun ports firing at something. At that close range the Radiance shouldn't last long...but if you look closely you'll notice that the missiles being fired by the LRM's overshoot their target and go spinning around to hit the Radiance and sometimes miss. If another capital ship is available it will jump in and go right into the middle of the LRM blob while an earlier, probably heavily damaged, Radiance retreats. The trick is to watch and see how much damage those LRM's are doing and then taking appropriate action to issue a retreat order to a heavily damaged ship before you lose it. Because the enemy will pursue a heavily damaged capital ship it is important to have a pair of repair stations standing by on that retreat planet and a well-prepared defensive force.
Alternatively, if I'm running Halycons instead, I just jump one or two of those in and give it circular move commands so it's running at top speed around the outer rim of the planet's gravity well. This makes it harder to hit. As soon as it completes one full circle I normally time a Progenitor jump in to match up with the Halycon to do shield repairs while it jumps out or another capital ship arrives for support if a single Halycon was used.
In the worst case scenario, those Disciples or Scouts will need to be called in for extra support. Normally several of those stay behind to play defense if someone has to retreat. I'll park them right where my retreating ship shows up so if a pursing LRM blob comes they're immediately fired upon. By this time the blob has taken such severe damage it either has to fall back or we're both sending reinforcements. This is where things get unpredictable and capital ships may have to retreat even deeper into allied territory. If that happens, it's important to go get and build phase jump inhibitors as quickly as possible to make sure that LRM blob never makes it back home or is unable to pursue.
EDIT: BTW, depending on the level of the Progenitor, the more research put behind it's damage propagation ability (I forget its name) the better since attacking a couple of ships will hurt the entire LRM blob.