From the British FCO Webpage of star_world's link:

"You must pay an airport departure tax of 25 Convertible Pesos (CUCs) per person when leaving Cuba. This must be paid in local currency."

This would constitute "spending money in Cuba" in violation of US law, esp. since it goes to a Cuban govt. agency.

Please note that 1 CUC is pegged as = $1.08, but US$ exchanged in Cuba are subject to a 10% penalty tax, so U will pay about $1.20 for a peso. This penalty may be avoided by bringing Canadian $, English pounds (no Scottish or N.I.) or Euros.

Especially those that have big ships run through them...

Huh? Did you even read the BOS-DCA-SAN stopover thread? It's apples and oranges to this issue.

I'm really surprised you could book through because even Mexicana won't allow Americans to buy tickets to HAV onliine. You have to do it in person and not in the US. Unless you are under a special exemption, such as family visit, education or media junket, you are presumed to be spending money in Cuba the minute you land and violating. Yes, there is the airport fee of CUC 25, which translates into about $30 at the bloated official exchange rate, that is built into the price of the ticket, at least when you go via Cubana. (If you want a real aviation treat, try taking one of their YAK 43s.)

Well CM uses onepass, i'm pretty sure you can redeem if you're not from the US.

Somewhere around 1998 or 1999 the US government agreed to allow US airlines to pay the overflight fees to save time/money on the flights. Prior to that carriers did, in fact, have to fly around Cuban airspace.

Yes, but that will be a ticket on CM stock, which is different than a ticket on CO stock.

If you read the itin carefully, I don't see how this is an illegal ticket, except if a US citizen actually tickets it. We don't know if it actually would have allowed the ticket to process with a US address, and I don't think the OP specified if it was or wasn't.
1. From the DR to France, so no embargo in force on that route
2. No US carrier segments, just CM and AF
3. Wouldn't this be the same as going on the website of a Central American or Mexican airline and doing a basic reward search to/from/through Cuba? Without being logged and having your citizenship on file, they have no way to tell where you are from to prevent you from flying there. I assume a lot of other carriers would let you book for $ or miles without checking. In all practicality, why would LAN, et al. bother setting up a system to check and block US citizens from booking somewhere in South America to Cuba? It is probably easier to just block US-HUB-Cuba routings as not valid, like the 'invalid destination' we saw on the first post.

I know AA has a regular scheduled flight from MIA to Cuba.

Yes, but those are only charters for those of us allowed to travel there. I used Continental when we went for a visit 3 yrs ago. The bummer is that you accrue no miles for this trip since it is a "charter" flight.