Yes, if we take Clarke's description as truth, then it seems the evacuation doesn't match Mineta's supposed arrival time.
But could Clarke be wrong in his analysis?
It's not just Clarke. CNN, the source put forward by George Washington & others in support of Mineta, also says people only started running out after the Pentagon was hit. NBC said it was business as usual, too. I've yet to find a single person or report that supports Mineta's story.
Incidentally, the ABC example you put forward to gumboot as supporting Mineta, actually does nothing of the kind. Whoever put it up carefully edited it to conceal what the documentary actually said. Here's the transcript:
04:01:40 KARL ROVE, WHITE HOUSE COUNSELOR
The President said, I need to, I'm gonna need to make a statement before we leave here.
04:01:44 BYRON MITCHELL, EMMA BOOKER ELEMENTARY STUDENT
He was red and I seen that had tears in his eyes. So I knew something bad had really, really happened. His face was just red. And he was, his lips were just trembling.
04:01:55 MICHAEL ANDREWS, EMMA BOOKER ELEMENTARY STUDENT
He kind of stuttered, when he talked, and he kind of said it all slowly.
04:02:00 PRESIDENT GEORGE W. BUSH, UNITED STATES
Today we've had a national tragedy. Two airplanes have crashed into the World Trade Center in an apparent terrorist attack on our country.
04:02:12 CHARLES GIBSON, ABC NEWS
(VO) Quick good-byes, and then a race to the Sarasota airport. At that moment, in the White House, . . .
04:02:19 VICE PRESIDENT DICK CHENEY, UNITED STATES
I was in my west wing office.
04:02:21 DAVID BOHRER, WHITE HOUSE PHOTOGRAPHER
The Secret Service had come in, to his office. I think it was two or three agents, which is very unusual.
http://911research.wtc7.net/cache/pentagon/attack/abcnews091102_jenningsinterviews.html
The clip you offered starts with "at that moment", and Bohrer's comment. But look at it in full and you can see they were saying "at the same time as Bush was speeding to the airport" - after 9:35. It does NOT support an early evacuation of Cheney, in fact it confirms the Commission account.
Could people have been running out of the building when Mineta arrived?
Of course. But then we have a problem. Mineta doesn't say there were one or two people, he says "everyone" was running out, from at least two buildings, the White House and the old Executive Building. For this to work, first we must believe that there were a few people coincidentally running out of both buildings as he arrived; that there were enough that he could believe it were a full evacuation; yet not actually enough that any of the media would notice this.
And for an example of what they saw,
go here, scroll down to the videos, and watch the "CNN raw footage" video. You'll see one or two people run by, then a group, then a security guy tells the media to get off the grounds, then someone says "explosion at the Pentagon".
Since you don't believe Mineta at this very moment, what evidence would it take to make you change your mind?
What evidence would make you come to the conclusion that Clarke has got it wrong?
It's not just the evacuation issues. There are also these.
#1, Mineta said he received a phone message from Garvey before he left his office, saying Delta Airlines couldn't account for all their planes. If they were talking about Delta 1989 then that didn't make the "hijacked" list until 9:30-ish. To believe Mineta I'd need to know what that Delta call was about.
#2, Clarke said Mineta hadn't arrived when his video conference began. He confirms in three ways that this was after 9:10 by a) having Garvey say Flight 175 was one of the crashed planes (wasn't confirmed until much later), b) having Garvey say there were 11 possibly hijacked planes (I've not seen this reported prior to 9:38), c) saying the FAA were "frantically looking" for Mineta (totally unnecessary if this were 9:10 as Garvey had been in Mineta's office less than 7 minutes earlier). To believe Mineta I'd need to know how any of that were possible.
#3, Mineta says he gave the order for all planes to land at 9:45. Both Ben Sliney and Monte Belger say Sliney did it, though, and there are stories that Mineta knew nothing about the order until some time afterwards when he made contact from the White House (which breaks his timeline as he says he's talking to Belger for the approach of Flight 77). To believe Mineta I'd need an explanation for that.
#4, Mineta apparently now says Lynn Cheney was in the PEOC when he arrived, but how is she going to be there before 9:20? She's said she arrived after the Pentagon was hit in interviews since around October 2001, anyway, long before any of this was an issue. To believe Mineta I'd need some evidence that this wasn't true (not just assumptions that she must be lying because of her surname).
There are other things, like the 9/11 Commission documentation for their timeline, but confronting these would be a good start.