Funny.... I am watching FIRST CONTACT this morning. In the start of the movie Capt. Picard got radio traffic that a bunch of Starfleet ships were engaging the Borg and gettiing thier rear ends handed to them. He was on orders to NOT engage but CHOSE to disobey that order and "entered" the DSE to help. Note the word CHOSE.

So...if I am on a mission...that could be considered orders from SF command. To enter a DSE I should have to CHOOSE to disobey orders and enter...again key word CHOOSE!!

End the auto-DSEs!

No, the person in your quote has it exactly right. Yes, like your First Contact example, you can choose to join a battle that's already in progress (those are the little red stormy icons with all the tiny ships orbiting them in sector space), thereby "aiding your fellow Starfleet officers", just like Picard did at the Borg engagement. It is indeed your choice when it comes to those types of deep space encounters.

What you can't choose is whether or not an enemy ship intercepts and attacks you (those are the enemy ships moving around in sector space). You can attempt to evade them, you can attempt to outrun them, but you can't hail them and say "Sorry, now is not a good time for me", when they jump you and demand your head on a pike.

DSE-style encounters exist in every MMO - we know them better as "random MoB who jumped me while I was traveling through the environment". Whether it's a Klingon vessel, a Defias Cutthroat, a Goblin Leecher, a Mechdog, or a Charr Hunter, you don't always get to decide when a hostile NPC interacts with you in an MMO. I think the only game that allows you to do that is Free Realms, which is an MMO aimed at children.

It's bad enough they allow players to warp out of DSE's without destroying any ships at all. At a bare minimum they should require you to defeat at least one group of enemy vessels before attempting to warp to safety. I think I've been pulled into a DSE against my will maybe once in all my time playing since beta, and that was when a Borg cube spawned on top of me in sector space. But some of my friends.. they get dragged into DSE's all the time. I once asked them "Do you think you'd be better at completely avoiding those if you had to spend time fighting inside before you could escape?", to which they said "Uh, yeah.. because then I'd actually have to take them seriously.". See, that's the difference.. I take them seriously now, which is why my efforts to avoid them are nearly always successful.

I don't mind roaming mobs, but roaming load screens do kind of get on my nervs a bit though.

Perhaps they could do roaming mobs that pulled you into episodic missions instead and save the DSEs for optional raid missions.
Perhaps even roaming mobs like you might find in other games that you could fight outside of an instance such as coh for example that had both instancing for missions and mobs outside the instance that could be killed.
Perhaps if the DSEs just had a little more depth to them instead of just kill "X" groups, some sort of game altering tidbit about them like some sort of special vendor unlock and so forth based on how many DSE runs were knocked out by your faction that day.

Of course some of the above would not stop people from being pulled in when they did not want to go, but it might at least take some of the edge off.
Just some ideas for whatever they are worth.

If the mobs were just roaming mobs you could kill right on the spot without loading into an instance I personally would not care, it's just all the load screens that start to get on my nervs for these encounters, but I will live if they don't change it.

Yes please, I hate the loading screens, and the interruptions when I'm trying to get somewhere a fleet mate is waiting for me.