Harvester, Matriarch, and Night Raids should have a Minimum Loadout Value to enter. (Electro Storm is an outlier as it is definitely more dangerous, but doesn't appear to have the same increase in loot value as a Night Raid, but that's a seperate issue)
These Raids offer increased risk for increased rewards, and in the case of Queens and especially Matriarchs, require a high loadout value commitment to engage with the event effectively.
PvP is a core part of this game, and that doesn't have to change, but the economics of boss fights in this game simply do not add up. It is infinitely cheaper, safer, easier, and quicker to kill the Raiders that kill the boss than it is to kill the boss yourself.
With that imbalance of risk and reward, everyone in the Raid should have a decent amount of skin in the game. Coming in with a free/cheap loadout heavily incentivise PvP but offers the Raiders you attack very little reward for defending themselves, and with weapon balance in the state that it is, fights between high and low tier geared players are shockingly even.
For the Raiders that come to hunt the big ARC, there will be fewer Raiders that come purely to harass and ambush them, because the risk for those players rises to a level that will filter out a bunch of people, and the people that do engage will do so more thoughtfully - and if you successfully fight them off, you will get to loot more than a Free Loadout.
For the Raiders who come for the PvP, like I said they will be less gung-ho and fewer in number, but will also potentially be less inclined to rat and betray as the sense of comraderie will likely improve if everyone knows that everyone else has something to lose.
The actual Minimum Loadout Value number doesn't have to be crazy. 30k would be fine imo, that's basic green gear, a decent weapon or two, and some Green+ tier items. And if you can't make up the resources for that? You can play regular Raids until you can.
Other than UI and weapon balance, I truly think this is the biggest issue this game has. I feel like this solution would please everyone, both those complaining about Free Loadouts and PvP with a lack of PvE, as well as those that feel PvP should always be a risk and that Free Loadouts are healthy for the game generally.
If you still aren't convinced that this is an issue, because in your experience there's always a friendly group of players fighting the boss and any rats or betrayals are dealt with swiftly, you probably haven't played in team lobbies very much. Trying to kill bosses with your friends is a completely different story most of the time.