(Let me first say, Culann: Arrowhead Pride, baby! Grew up in central MO plus served at Whiteman AFB in western MO.)
One other sci-fi universe that kind of does away with all-guns warships is the Honorverse, with all non-carrier* capital ships being almost entirely missile launchers (including massive saturation missile pods). It actually does a great job of envisioning a combat environment that demands exceptional point defense, because a battle could have a hundred or more missiles fired at each (super) dreadnaught, with only a handful of hits necessary to wreck its day. (Which is weird considering the basis for the series (Admiral Lord Nelson/Horatio Hornblower IN SPACE!) is all about warships hitting each other dozens of times each before succumbing.) Missiles at the beginning of the series are capable of powered flight (engines firing the whole time) of 6,000,000 km (20 light-seconds), whereas lasers and grasers (gamma laser) had effective ranges of 1,000,000 km versus an unshielded opponent or half that with shields ("sidewalls" vs. the acceleration "wedges" that were totally impenetrable).
*The Honorverse does have carriers in the form of CLAC super dreadnaughts (over 1,100 meters) with Light Attack Craft (~70 meter long each, 100 per CLAC), but they're mostly secondary to missiles. LACs have a mix of a single graser (cruiser-class!), a few smaller offensive missiles, and some counter-missiles and laser PD mounts. ("Cruiser-class" is a bit of a misnomer, as their ship-class structure goes Destroyer, Light Cruiser, Heavy Cruiser, Battle Cruiser, Battleship, Dreadnought, Super Dreadnought, with smaller classes barely mentioned.)
I am not, however, recommending going to a no-guns combat environment for Stellaris, and I'm also not recommending going to (or staying in) one where defenses against SC and GW have to be suffocating in order to keep balance with the effectiveness of direct-fire weapons against their matching defenses. I'd prefer a system where SC and GW can eventually overcome their chosen defenses, like lasers getting past shields or kinetics past armor. without having to first destroy every single Flak/PD platform. Balance it for the greater effective range (not start-of-battle engagement, but actual fighting range), but let me fight on a fairly level playing field with whatever comparable weapon I want to play with.