The two-day trajectory is more defended because on your two-day trajectory everyone in the solar system sees you and where you are going, so the defensive fleet is waiting for you, or intercepts you. The idea that there exists a solution to "set up your vectors right" so that interception is impossible doesn't really seem to be a valid assumption.
The problem is simple. The stealth ship in question has to remain undetected until it's too late for the intercept to occur. The conventional ship has to come in too fast for the intercept to occur. If the defender can have a fleet on station in 2 days, then the stealth ship must remain undetected until 2 days before it strikes. Actually less, unless you want to lose the ship. I find that sort of thing (over a long mission, no less) hard to credit.
I agree that there is a little bit of hand waving, but if you filter out the existing plasma and only let out the helium that have already emitted their photons to leave their excited state then they aren't going to randomly reignite into plasma once they leave the reactor.
The plasma will remain as plasma until after it leaves the reactor. Your problem is twofold:
1. Filter out only the parts you want to eject (magic).
2. Cool it enough to remove its signature without rendering it useless as an exhaust (even more magic).
This goes way beyond handwaving to the realm of the impossible.
That's not true. If the stealth ship is detected two months into it's journey then it is two thirds of the way there. It fires up its normal engine and gets there in ten days, the stealth system gave it 20 extra days to play with the Sorium harvesters and begin their escape trajectory. Sure the fact that it has a normal engine and a stealth engine may mean that its shields are halfsize, or it doesn't have as many weapons. But how many weapons do you need to destroy undefended Sorium Harvesters in twenty days?
I'm not sure where you're getting this from. You would get 20 extra days, assuming it takes the enemy 30 days to respond. But they will take 30 days to respond
from the detection of any ship. Period. Thus, if I can get a conventional ship to the harvesters within 30 days, I can use it, too. Based on the above numbers, it takes twice as long to do something with the stealth drive as the conventional drive. What if I replace the stealth drive with more conventional drives, and use that instead?
And you keep forgetting about this thing called "escaping". That's going to be an issue for any stealth ship.
The question is not "can it be made to work under certain circumstances?" The question is "will it work better then the alternatives?"
(And my alternative involves long-range missiles. They put the ship at less risk, and don't give any response time.)
Edit:
Two more serious problems occurred to me with the example given:
1. This is Newtonian Aurora, not regular Aurora. The stealth drive will not have half the speed of the regular drive. And if you have 20 days left on stealth drive (assuming constant deceleration) then it is impossible to stop at the target within 10 days. Why? The acceleration would have to be instantaneous. Assuming the normal drive has twice the acceleration, the ship will arrive in 15 days, coasting for 5 and burning for 10.
2. You're assuming that you know when you've been detected. That's not a smart assumption. And dealing with a stealth ship that thinks you don't know it's there is easy. Launch a long-range missile salvo at it, and have it go silent for most of the run. When it gets close, it goes active, and kills the SS. And since the SS isn't using active sensors, it will probably first learn of the missiles when they come up on thermal, which is usually too close for effective defense.