As someone who recently did a 2v2 tournament I don't think balance is your primary issue. Rather you'll run into the problem of having to find and equal number of people who play both factions.
If you are scraping the barrel to get enough on one side you might have to settle for second tier players for that faction.
At the same time having an overwhelming amount of players on the other faction leads you into the problem of who you are going to include.
Will there be cherry-picking perceived good players or will you have a draw? The risk of having sub-par players fighting against really good ones will be there and that might be a problem.
You have the same issue if you demand players be from different nations, more populous countries have a bigger pool of players making it more likely to find a good German than a good Luxembourgian.
If you only allow 1 team from each country into the main tournament you will have to "cherrypick" which German team enters or have some sort of qualifier round, whereas with Luxembourg it's unlikely that many teams will join and so get a free pass even though the quality might be below that of the German teams who has to play, and won't pass, the qualifier.
Or require the players to play both factions and take no consideration as to nationality and avoid the problem entirely.