You've actually got an interesting question once you get past the non-starter with trying to find a use for the SL junk other than using it to probe a star's innards. Science can always find a use for military surplus.
How do you defend a wormhole terminus? The classic answer has been with forts - big, slow monsters that can take a lot of punishment while bringing the big guns up and converting the attackers into navigation hazards.
I wonder if that's the best approach in a universe with Moiarty and Mycroft system defenses?
A wormhole terminus/junction has two threat vectors to worry about.
1) Through the wormhole. This hasn't been a real problem since the invention of effective laserheads. The standoff range of a laserhead missile lets it detonate from outside the grav turbulent entry lane (where a physical missile would be instantly destroyed) but still strike ships caught within that lane under sails.
With contact nukes you couldn't use missiles against transiting ships until they cleared the lane (and could bring up their wedges and sidewalls) so you had to have forts parked within energy range to contest the entry. Now those forts still had a massive defensive advantage because they had sidewalls and the attackers didn't - but it did force them to be in pretty predictable locations.
2) Through hyper. Wormhole termini are invariably located beyond a star's hyper limit and their own hyper limit is very small. So there's a risk that an enemy will successfully pull off what the Peep's did during the Basilisk raid and drop out of hyper on a rapidly closing vector - allowing them to quickly force defenders into an energy duel. That, I think, is probably the primary reason that you still have big nasty forts (albeit now ones for Manticoran systems with LAC bays, Keyhole II, and Apollo missile pods to deploy)
I doubt even in time of war that Manticore would be willing to turn a terminus defense entirely over to automated computer control -- especially with no humans close enough to attempt to override. So even with FTL comms you couldn't control Junction defenses from Manticore; the 7+ minute FTL comm lag is too long to be acceptable even if all you're sending is an "auto-fire approved" message. Ideally you want to be able to lay fire on a hostile emerging in your wormhole's entry lane in under 60 seconds - so you've got enough time to destroy a potential mass hostile transit while they're all still stuck under sails. And that may be as short as a couple minutes.
So even if you have zero comm lag you need your laserheads parked within 1.5 million km just due to time of flight. In that scenario you don't even need MDMs because you barely use up the first drive at full power. And for snap shots against an enemy who successfully pounces from hyper at near-minimum range you also don't need long range missiles - but you'd still want them in case (as at Basilisk) the enemy failed to jump accurately enough.
So I think, even with FTL, you'd want manned forts fairly near the terminus, say within 10 light minutes, to control the launch. But that's still further away than un-relayed Apollo, can control a missile. Hopefully dispersion, randomized patrol patterns, and stealth would keep an enemy from knowing where to try to ambush the control forts and they could use Mycroft with minimal control lag to order pods near the exit lanes to engage anyone idiotic enough to try a hostile transit but dispersed Apollo pods to engage attackers smashing through hyper.
Still, not having big armored targets to focus the enemy's attacks at the wormhole might
mean that whatever civilian stations there are to handle servicing, warehousing, docking, bars, etc. might take the brunt of any pounce from hyper attack - not sure if mitigating that's a good enough reason to keep fairly close in manned defensive forts though.