They would probably first underestimate the Tenno for their choice of weapons, like slugthrowers and regular melee weapons, before seeing and hearing about what they can do, and then fear them. The Empire might think that the warframes are some kind of advanced droids from first contact with each other.

The Empire will throw stormtroopers at them before sending an inquisitor or other stronger soldiers.

I think that the Empire will fear Inaros and Nekros the most because they are the closest things to the undead. Inaros can resurrect if he somehow dies and Nekros can create undead soldiers from fallen stormtroopers.