What sorts of idiots work for the post office today?
I just got a multiple book package returned back to me covered in warning stickers and keep away from aircraft stickers.
The gist was that it was over 13 ounces and stamped, therefore must be mailed at the post office.

Except I did mail it at the post office.
Was I supposed to wait in line and hand it to them at the counter?

It was also marked media mail, so if someone was so concerned about the contents, they could have just opened it up!

The question in your first paragraph is rhetorical, so I'll skip it and answer your second question.

Yes.

The easiest thing to do for a package over 13 ounces is buy some or all of your postage using the APC, you can enter any value you want to buy so if you know the rates for the MM your sending, you're good to go. You can do a mix of stamps and electronic if you want. There just has to be something trackable if you don't hand it off in person. Or you can buy postage online or at the counter.

Yes, if using stamps, you must hand over any package over 13oz to a counter person.  If you can't, or don't want to, wait in line, you can use online printable prepaid postage and then mail from home, a blue box, or any other drop location.

This is directly from the "Help Center":

Do I have to mail from a post office?

The gist was that it was over 13 ounces and stamped, therefore must be mailed at the post office.

Except I did mail it at the post office.
Was I supposed to wait in line and hand it to them at the counter?

Yes.    You have to hand it to a clerk at the Post Office.  

It is more of an FAA rule that the Post Office has to follow if they want to keep putting their mail on airplanes.

When I go into my Post Office with this kind of package, I wait at the side of the line, kind of holding the package up, stamp side toward them, until one of the clerks sees me.  S/he tells me to leave it on the counter, and continues helping the person in front of his/her window.  I don't know if they do this for everyone, or if they recognize me, but it's nice.

Patty, yes, it's because they recognize you. They are really supposed to ask the questions every time and check the postage, but most window clerks will let you slide after the first time or two. 

Yep! I always wait in line and I like it because I buy my postage online so the tracking is always tacked on. The receipt that I get from the post office is my own proof of mailing. I'd be too paranoid to just drop the mail at the PO boxes because of that same situation of, "what if my digital scale is wrong and I'm short on postage?"

Again, another yes. 

Like Patty, I wait off to the side until I catch a clerks eye between customers.  I hold up the package and they will usually wave me over and accept the package...over the counter, accomplished.  If this is your only transaction, you shouldn't have to wait in line (or at least use the express line).

FYI - Thought I had heard the 13 oz. rule was Homeland Security. 

Actually, the 13 ounce rule started during the time of the UniBomber.  Before Homeland was formed.

Some rules are written in blood meaning something bad happened to make it necessary to make the rule. They want to be able to have have a trail to track down someone who will commit crime. 

It is the FAA's rule.  They don't want anything dangerous to fly on passenger planes.