I think even in early interviews, before leaving DC, Moore had said that he put the ending there so there wouldn't be a sequel. Whether that makes sense or not, he's always claimed that. I recall reading that by his own admission the only possibility for a "sequel" would be a comic based on the Minutemen, but even back then he didn't think that would happen. Oddly enough, in this interview (or maybe another from the same period) he mentions that the movie rights have been bought and you get the vibe that at the time he thought that was a good thing (though he doesn't specifically say so).
Back to the point: wasn't the whole reason they asked him not to use the Charlton heroes that the ending would leave them "unusable"? Not that there isn't always a way to force a sequel if they think it'll make money (see: 300), but still, that goes to show how definite the ending is perceived to be.
About Barry Allen: the loophole is very simple, he was jumping through time in Crisis before landing in the moment of his death. Wolfman's idea was that one of those time jumps could leave in the time period after the Crisis, so he would know that any minute now he would jump into the past and die. This would give him a more extreme attitude and would possibly lead him to carry big weapons, grow muscles, get a cybernetic arm and hang out with big breasted women.
