I stopped making CTF levels a long time ago but I always cared about making levels balanced. I usually went for an asymmetrical style, since I think those types of levels are more interesting, but I always tried to make it so both sides have a good balance of advantages and disadvantages. I think I was successful with most of my levels. None of them are perfectly balanced, but I don't think any of them have serious flaws. Or, for the ones that did, I fixed them in later versions. My most balanced level is probably Helldome because it's the only perfectly symmetrical one (aside from the RF and toaster powerups).

I think the key is not to make a level that is PERFECTLY balanced but rather make a level that is balanced enough so that a player who is skilled can win over a player who is less skilled, regardless of team. And if the two sides are evenly matched, maybe one side gets an advantage, but it shouldn't be big enough to be decisive.

I say this because (a) it is very difficult to make a perfectly balanced level, unless it is perfectly symmetrical, and (b) levels are usually more interesting if there is SOME difference between the two sides.

I think it's a bit pointless to worry about a level being slightly skewed. Consider that pretty much every game that's played (video game, sports, board games, etc) tends to give one side an advantage. For example in sports the home team gets a bit of an advantage, and in chess white has an advantage over black due to moving first.