Short Answer: No
It definitely does not count as ranks; it is a bonus. It’s effectively equivalent to the Skill Focus feat (which also provides an untyped permanent bonus). It does stack with Skill Focus, though, since they are different (and also does not count as Skill Focus for requirements, though I recommend houseruling that one).
A character’s number of ranks in a skill is based on how many skill points a character has invested in a skill. [...]
Each skill point you spend on a class skill gets you 1 rank in that skill. [...] Each skill point you spend on a cross-class skill gets your character ½ rank in that skill. [...]
In short, if you haven’t spent skill points, they aren’t ranks. There is exactly one exception to this (a poorly-considered feat from Cityscape) which explicitly states that it gives a single bonus rank.
Recommendation: ban anything that does let someone have more ranks than the normal limit
Skill ranks are very hard-and-fast things: you get a very specific number of them based on class and intelligence, they are placed once and locked in place, and most importantly, they have a very fixed maximum based on level. They are constantly used as a kind of “level-gate,” requiring you to be level X by requiring X+3 ranks in a skill. Skill points tend to be fairly cheap and skill requirements are usually pretty easy. In most cases, the only reason they exist is to force that level to be the minimum before taking the feat or prestige class.
There are some tricks for getting around this requirement (though Knowledge Focus is not one of them), but in most cases I would strongly recommend against allowing them. The level barriers on feats and prestige classes are important.
Except... maybe for a truenamer; they are that bad
Since your player is playing a truenamer, you might consider making an exception. Actually, you might consider totally revamping the truenamer, perhaps using one of the high-quality homebrew fixes out there. Kellus’s homebrew fix and Kyeudo’s homebrew fix are quite well-received.
Because with the Tome of Magic truenamer, we are talking about a class which is literally incapable of performing the things its description says it can do. Anyone who reads the truenaming chapter of Tome of Magic and makes a character with levels in truenamer, assuming that their character will work as Tome of Magic describes it, is in for a stunning level of disappointment and frustration. With a lot of optimization, you can get access to some really mediocre tricks; without optimizing, you could find yourself only barely able to do anything better than a commoner can.
Zaq, quite possibly the world’s foremost expert in the class, has written about his experiences playing the truenamer here, and then went on to write In the Beginning Was the Word, and the Word Was Suck:
A Guide to Truenamers.
I encourage anyone who is considering the class to read his experiences: he managed to make a truenamer that was reasonably fun, but it took an enormous amount of work, was only barely effective, and he was constantly running into problems of poorly-edited rules, unexplained features, crucial information that was outright missing from the book, and so on. After six months, he retired the character in frustration, despite massively enjoying the character himself. The mechanics were just that obnoxious to work with.
So seriously, please very strongly consider using one of the homebrew fixes. Failing that, letting your player into a prestige class early is among the least you can do.
1 All statements about truenamers being weak have a major caveat: at level 20, the truenamer suddenly and immediately becomes the most powerful class in the game, because it gains the ability to cast gate more-or-less at-will, twice a round, and can teleport to anyone who mentions his chosen nickname as a non-action. This does result in a hilarious interaction if you choose, say, “What” for your nickname:
BBEG and henchman are talking:
Truenamer appears out of nowhere, summons two solars, and disappears
BBEG: What the hell?!
Truenamer appears again, summons two more solars
Truenamer: “Say ‘what’ again, I dare you, I double dare you, mother—!”
Truenamer disappears again.