I haven't found this anywhere, so here you in are:

Friendly Fire:
in Rome's data folder (Total War ROME REMASTERED\Contents\Resources\Data\data), you'l find the file data_controlled_features.json.
inside is the option: "disable_friendly_fire": false, which you can simply change to "disable_friendly_fire": true, and your archers will now stop firing at your own troops in a melee! (well they'll still fire, but not damage your guys)

Removing Rebel Merchants spawn:
still in the data folder, there are 2 files!

- descr_campaigns.txt
where you find the line "rebel merchants": true, to be changed to "rebel merchants": false, (not 100% sure that really does anything, not on its own anyway).

- and descr_mission_modifiers.txt
 where you'll find the folowing block
// Rebel Merchants
REBEL_MERCHANT_LIMIT :: 30
REBEL_MERCHANT_SPAWN_CHANCE :: 5.0

change both values to 0 and rebel merchants will stop popping out of nowhere (this must also lower the rebels' income so you might want to get them a boost elsewhere).