I don't think anyone's accusing you of being in that situation. Most of us (I think) are responding to the exec's response, not accusing you of handling the situation unprofessionally. I wanted to make that clear because I think everyone here is trying to help you rather than accuse you of being a newbie or somehow behaving inappropriately.
Yeah, that's pretty much exactly how it goes sometimes. Most execs even use their work email in that situation.
This part isn't. "Protocol" and "strict company policy" are systems in place to prevent or curtail unsolicited submissions. Believe me when I say that no one
in a position of creative authority in this industry would keep his or her job for long if they refused to read a great script because it didn't follow a rigid and inflexible submission process. Maybe there's a submission release to sign along the way, but if it's a great script, that's all that matters.
Creative execs are lauded for finding great material, not slapped on the wrist for failing to follow a rigid submission policy. Here's the important part, though... if you're being told that there's a strict submission policy in place or that they'd love to read it but their hands are tied... it's all a polite way of saying, "I don't want to read your script." If they did want to read it, they would have asked to read it. There is no company policy anywhere in the industry that says, "If you come across a script that catches your interest, you can't read it."
Having a manager or agent is irrelevant if it's a great script. People in the industry make deals with writers all the time regardless of whether they have reps, are guild members, etc. It's all about the quality of the script. If you've written a great script, it doesn't matter to them whether you pay a rep 10% or not.
You had it 100% right a minute ago. If he really wanted to read it, he could. If he really wanted to refer you to someone who could submit it on your behalf, he could. But he didn't. Don't rationalize the situation by thinking he doesn't have time or it's just because he has to follow some arbitrary submission procedure. You had it right the first time. If this guy "REALLLLLY wanted to read it," he could. But he didn't ask to read it, nor did he refer you to a manager, or offer any special consideration other than "submit it just like everyone else." That's a pass
Just out of curiosity... if your partner is a seasoned, optioned, produced working writer... does she have a rep that can submit it for you?
I don't want to (and hope I don't) come off as particularly harsh or combative, but I see the direction this train of thought is headed in. Believe me... I've been there on both sides of the table. Regardless of the circumstances of the meeting, the bottom line is that this guy heard your script premise and had a chance to say "send me your script." He didn't. Instead of saying, "Send me your script," he said, "Submit it through proper channels." That's a pass.
You can justify it by saying it's punting, or that he's just a guy following company protocol, or that he's an exec who's probably very busy and can't read it right now... but the honest truth is that if he's not saying, "Yes, send it to me," he's saying "no." There are a million nice ways to say "no" to someone (and I've even used the 'strict policy' and 'I'm very busy right now' excuses myself on occasion)... but it's still a no.
If you truly believe this script is right for this company, then do what you have to do to submit it through "proper channels." Heck, why not try to find an actual manager or rep rather than someone who will just submit this one project for you? Just please understand that you don't have any special "in" with this executive or this company, so don't go out of your way to parse his response looking for underlying meaning. He didn't bite when he had the chance; it's as simple as that.
Best of luck to you and your partner on your writing endeavors!