Obidiah’s plan was always “a new world order” as he said. Remember he left a resignation letter with Tony before taking his heart-reactor. That was the alibi. Later, in a power suit he was in the arc reactor room when the battle began, and they cracked the containment glass. The reactor started to overload.
Tony reminded Stane that “you know when that reactor blows a lot of people will die.” Obadiah does know this, so there was going to be no evidence.
The government was not going to let the Iron Man project go public and Obadiah also knew that - he traded weapons all the time. You recall the Air Force started their cover-up during the aerial fight:
OFFICER1: Get me Major Allen. Scramble the jets!
OFFICER2: Not necessary, people. Just a training exercise.
OFFICER1: Yes, sir.
After Stane died they created a massive coverup alibi, even getting 50 “witnesses.”
You've all received the official
statement of what occurred at Stark Industries last night. There have been unconfirmed reports that a robotic prototype malfunctioned and caused damage to the arc reactor.
Fortunately, a member of Tony Stark's personal security staff...
So if Obidiah killed Ironman and Pepper everything else was going to be destroyed by the arc reactor. The only thing left would be the power suit, and a government cover-up. Obadiah would be free to sell the technology.
We don’t know if Stane planned to blow the reactor, but he went there for a reason and it certainly worked to his advantage. At that point he wasn’t really worried about leaving evidence. His plan was simply kill all witnesses and blow the whole place to bits, then “some unknown robot suit” would fly away with the resignation as his alibi. It’s a fairly typical arch-villain plan.