I think the damage the aliens have done to trade routes is similar to what Germany did to Britain in both world wars when its submarines attempted to blockade Britain and starve it into surrendur. Neccessities of life such as food, and materials necessary for the war effort had to get through, regardless of the cost in lives, and the result was the convoy system. Even so, just about everything had to be carefully rationed.
After the first terror attack on a major city, there will be no chance of covering up the fact that aliens are behind the sinkings. Fear of the aliens will make shipping insurance impossible to obtain and ship owners will refuse to risk their ships for the duration of the emergency unless they have a massive military escort and a promise that the government will compensate them if their ship is lost.
Unfortunatly, X-Com is not going to be able to give a swift victory over the aliens, so national governments will be forced to introduce rationing. A combination of rationing, high inflation and increasing unemployment will force the governments to go over to a wartime economy, in which the manufacture of military hardware gains priority over consumer goods. Under these circuimstances, it is perhaps understandable that some governments would do a deal with the aliens and let someone else do the fighting.
Under these circuimstances, I doubt that national governments would be happy about giving X-Com political and (some) financial support, and then being told that if they want to get the benefits of the technology X-Com has developed, they are going to have to pay. As the prevaling view seems to be that selling to terrorists is out of the question, the only option I can see is for X-Com to do a deal with arms manufacturers such as Heckler Koch, who would be doing quite well out of the war. It is quite common for a modern assault rifle to be manufactured under license in a lot of different countries, so X-Com would have to work out a similar deal for Gauss weapons, aquaplastics and underwater medikits.
There is the danger that X-Com would get ripped off. However, they can point out that ripping off their patents means that they would have less money to protect the world, so some countries would regrettably end up being thrown to the wolves. It's moral blackmail, no matter how many times X-Com's spin doctors use the word "regrettably", but politicians pull the same stunt on each other all the time. Besides, they would find the prospect of X-Com eventually becoming self-funding appealing.
The zrbite issue is a problem with manufacturing alien weapons, however Dr Zager has developed the power cells that make laser and gauss weapons practical, so I think the problem can be solved if the commodore asks him nicely