As your GM, I would say that both feats are excellent choices for any character in this campaign. However, I would suggest Imperial Military Training has a higher benefit right now.
It is likely that the longer the campaign goes, the more force users you will encounter. Early on, if you are affected by mind-affecting effects, they might be the result of abilities that are not force based. Many noble talents, and fair number of scoundrel talents (and a few soldier talents) do afflict targets with mind-affecting effects. Unstoppable force would be useless against such abilities, but Imperial Military Training will counteract them.
Also, if you do manage to get into hostile encounters with force users early in the campaign, your will defense won't be high enough, even with Unstoppable force, to guarantee that mind-affecting power will fail to affect you. Imperial Military Training on the other hand could prove its worth in such a situation. In an espionage campaign, you should fear the Mind Trick power above all others. Imperial Military Training is an excellent defense against this power.
Not all mind-affecting effects are worth bothering to negate via Imperial Military training. Some affects are a byproduct of an a standard action attack, or the result of a swift-action ability. These kind of effects may often be minor annoyances because they are essentially riders on an actual attack. You can conserve your use of this feat for a more serious instance. If someone dedicates a standard action or a full-round action to afflicting you with a mind-affecting effect, then that MA-E is probably serious enough that you want to activate your Imperial Military Training.
Also, there are 6 of you guys. It's not terribly likely a single player will be bombarded with multiple MA-E's over the course of an encounter while the rest of the party is ignored.
As for things going pearshaped for messing with the nature of "an encounter" I'd like you to back that up, Unbeliever. I have run Saga before and I am confident that almost nothing could be worse than running encounters via the RAW "definition."
I have told the players that a single encounter could span multiple combats and that they should evaluate abilities that last for an entire encounter more favorably, and evaluate 1/encounter abilities more harshly. Players can also gain additional uses of of 1/encounter abilities by spending a force point (we use the daily force points variant rule from JATM) and force powers no longer recover after 1 minute of meditation, they recover at the end of an encounter like any other encounter ability.