Right, point by point:
1. Why does it matter if it's 1 or 50? What matters is the intent right?
2. What makes you think this isn't so? FIFA has a 5 year residency rules right now which is seperate from any nationalisation rule because, as far as FIFA is concerned, living for 5 years in one country makes you as good as a national. So right now citizenship doesn't matter in regards to this issue. If it did, if FIFA required citizenship, then it would depend on each country's own nationalisation process, on which FIFA has no authority whatsoever. And again, nationalisation takes precedence over sports. Even if FIFA had grounds to think something fishy is going on and try to ban the player, it sounds like it would be incredibly easy to appeal that decision on a myriad of grounds.
3. This already exists. Players cannot represent two countries in an official competition. Friendlies are not official and if you forced players to stick to their youth teams, you'd have players stuck playing for a country their foolishly chose when they were 15-18. They actually changed the rules a few years ago to fix this issue.
This isn't an issue with the rule, it's an issue you have with a specific incident. Changing the rules will just mean they get around a new set of rules. The only way I can think of that might solve the Qatar issue is investigating each player case by case in the hopes of finding some damning evidence that won't get laughed out of an arbitration court.
I've explained why this is the case above. If Deco can switch sides, so can these Qatari players. Qatar isn't forcing anyone. It could quite easily be a case of the South Americans being the ones to come up with it, and either way, good luck proving they aren't worthy of national status which is irrelevant anyway because FIFA doesn't care about nationality, but residency. If Qatar is inviting players to come play for them for FIVE YEARS and they agree, and play there for 5 years, they have every right to be capped. They've done their time, regardless of their motivation, they've lived in that country for 5 years, not much you can do.
4. I don't know if this is conjecture but I believe it is. Could you link to the article you're basing your panic about Qatar?