The skinny of the situations was/is as follows (need some insight as to what would happen)...

PCs ship arrives at a world - this world was a secret that some officials were trying to get fixed before anyone else notices (thus why naval officials asked the PCs for help) - in return their ship would be outfitted with Naval crew rather than the crew they had ATM...

So when they arrive at that secret world - all the people are long dead - and there's some sort of psuedo-scientific mold that "acts" like a neutrino (particles that can pass through matter) - suffice to say the PCs were "diseased" (the mold caused salt deposits to form in people's brains - countdown 28 days).

The PCs of course are surprised, upset, and confused - long story short - a special Imperial Guard Surgerical Force was deployed (as part of the deal) on the ground of said secret world. Its commander refusing to stop his mission or abort until he hits all 4 stragetic assets and gets to the bottom of the problem (he's all glory ridden like its better to die for glory than run).

So one of the PCs (as given by an NPC Magos - in his own ship acting as an attache to another "advenutre" not married to this one, persay - who gives the PC the option to liquidate the Guard commander - so he does, and at the end of the day the shuttle crash looked like an accident LOL)

Moving on - so the PCs grab the guard strike force and leave said planet - FAST FORWARD

The PCs and Guard are all cured by this point - its almost old news - ATM the Guard onboard were being led by a council of their highest ranking officers - totally 9...

Comes to a point where the PCs are in for a long stay at Footfall - repairs, adventures, etc

Granted at this point of the campaign their ship has been taking Morale hits for a while (part of the cure - the ship had to be taken through the Dancer's Roil to a "gate" which leds to something people call a Witch-Touched Star - there they were baptised in its light and thusly cured - BUT to get their the cre had to sing an Occult-based Hymn to course through the Roil to said physical "Gateway"

So by that point the Naval crew and the Council musta been scratching their heads like - who is actually commanding us?!

BACK TO FOOTFALL - Present DAY

So with all the Morale hits - one PC (an Explorator) wants the crew to take leave - in order to sure up some Morale; the council objects (also - before - when they passed by Footfall previously under the command of the assassinated Colonel - he refused leave in Footfall as well); they state they will not have their crew sullied, corrupted or otherwise victimized in such a foul port

(I run Footfall where the "true" Creed agents are in hiding - like "Cells" - AND authority like Arbites isn't existent in strong enough numbers to actually be the authority herein... I.E. Footfall is a black port in my campaign and the players know that)

So the Explorator demands of the Council to pick one member who will serve as an example to the rest - as he wants to put in a cortex bomb in that council members' head (and he tells them that in no uncertain terms). They initially on the radio with him get scared as Humans are prone to do - later on when he arrives back on the ship to carry out his plans - they balk and command the crew to stand against the Men of Mars (who to them must have gone crazy lol)...

The PC playing the Explorator thinks I ran the protocol incorrectly - and feel they should have complied with his desires...

NOW I do treat all the PCs as Peers of the Rogue Trader (i.e, his Partners not his servants) + the actual Rogue Trader is away amassing forces for the PCs to have a big fight to come...

So - would Naval crew fight a Mechanicus Explorator (Peer of the RT) on their own ship (to split hairs the Navy was brought on board of this ship) - or did I run this against the expected flavour of the 41st millennium?!

Please Advise

Morbid

People are free to act however they want to, and are allowed to act contrary to your Player's desires or what they think is logical.

From a fluff standpoint, they absolutely would. The bounds of the Mechanicus are to recover technology and service the great machines, but they don't have the authority to commandeer another ship - ESPECIALLY one belonging to the Astra Militarum. Once they start talking about murdering people to make examples to others, it is entirely reasonable they would stand up to that sort of perceived heresy.

Remember, when the Imperium starts to turn on itself Chaos begins to come in. Even if it's done for the best of intentions, the Imperium has done a lot of horrible things in the name of preserving their "unity".

Sounds like the salt deposits weren't completely removed. Apparently the chanting wasn't backed by sincerity.

Sounds like you ran it perfect to me. Hardened, Loyal soldiers dont want to listen to the wierd robo-guy who is literally demanding they turn on one of their brotherhood to appease his fit of pique. IMO never gonna happen. And the Navy guys would feel similar. Not to mention that naval ratings are likely voidborn and born into the fleet at that, they would be used to following orders and have a similar sense of us verses them. Idk how low morale is atm but too low and the explorator could be looking at revolt and or assassins. You could rule that they are eventually cowed and he manages to plant that bomb but id rule SERIOUS bad blood with not only that unit but anythey come in contact with. No one wants a boss who shoots you on bad days.

OOOHHHH!! and The Imperial Cult would have some pretty definite things to say about an Explorator who is attempting to force them to expose themselves to corruption.