Now, while the discovery is interesting in itself, it doesn't affect gameplay as much as you may think.
Personally, I usually never get to the point in a game where I have to get Observatory and Meteor Defenses. And if I get around to research them, I don't usually build them. Why ? Because they take up too many people on something that for my part isn't really worth it.
Now, while some new players enjoy being able to emp a "Mining Colony" (3 smelters and their vecs). Every player who has played for some time, know that this isn't really worth the cost of the EMP Missile. It's simply 3000 Common and 1500 Rare ore wasted on something that doesn't hurt your opponent that much.
Assuming however, that you are in a tight situation, and that you have a Meteor Defense somewhere around a important location.
My inital thought here is that someone must be pretty stupid to have his army massed around the MD. First you would have your front line of defenses, just about 1/2 screen behind, your second line of defenses(including the MD). Behind this again you would have a small back-up force just in case.
With this scenario, your opponent would have to 2 Spaceports up and running(swallowing 10 colonists)He would also have to have buildt 2 EMP Missiles, and have enough ore to build 2-4 more on the spot. (Talking ALOT of ore here)
In order for him to take out the location, he would then have to strike your 2nd line of defenses(taking out the MD), then strike the Frontal line with a Missile. Then make 2 more missiles, get ready to EMP your MD again, and then your front line (This time to hit even more vecs as back up forces are ready now) And continue Missile production and hitting enough vecs to break through.
This would seem like a costly and time consuming to me, and frankly only if everything goes according to pland would it work out. (Which things rarely does anyway)
All in all I would just recommend that you don't use a static defense, but have a good mix of Tigers and back-up Lynxes to deal with enemy threats.
And there are more ways to avoid EMP Missiles than just a MD