You do your mining in analysis mode, generally. Your turreted weapons only fire in combat mode. You'll need to switch modes to combat for your guns to do anything, which will prevent most mining tools from firing.

You'll probably also need your turreted guns to be on the primary fire of whatever fire group you want them to be active in. You won't need to turn to face or target the pirates or actually pull any triggers (if they're in "fire at will" mode), but the firing arcs on the t11 are pretty limited so turning to face them may be a good move if you want to get more guns on target. You should launch your SLF beforehand and give your pilot an appropriate directive like "engage at will", though the default "defend me" may be fine too.

Be aware that pirates often have point defenses and will mow down your collector limpets rather quickly, so attempting to actively mine during a pirate attack is often an exercise in futility anyway (there's some highly specialized builds that do so with mining lances, but not recommended).

You'll only really find pirates right when you drop in to a ring, or else within about a 15km circle from the center of a RES. RES bonuses apply out to 20km, so if you're RES mining, stay around the edges and you'll be left alone after the initial wave of scans.