Disliking having levels in a class forced on you can be a reflection of playing a character.
For example, his paladin might distrust arcane magic, perhaps seeing it as a prideful trespass on divine domain, believing that power without moral limitation leads to temptation and evil, or having had personal bad experiences with arcanists. The character thus would deeply dislike being granted any kind of arcane power, even if it's totally free.
Alternatively, if the new arcane class levels slow down the progression of other classes in some way, even a paladin who likes arcane magic may feel that this represents a distraction from their chosen calling. I know an engineer who was annoyed by the required "arts credit" in his degree program for this reason.
And I do think that giving a large power boost to only part of the party - or worse, the whole party but one member - is unfair, even if it's part of a story. Neat story-related power treats are great but it's not fun to be left out. The more significant the treat, the more important it is to be even-handed. Would you think it fair for a GM to introduce a multi-session side quest for each character's backstory, but leave one PC out? Not without confirming with the player that they didn't mind missing out on that part of the game.
While some people do are only about the story or only about tactics/build, most PF gamers I've met care about both and being significantly behind other players in power can detract from enjoyment of the game, particularly if you get to the point where the underpowered player feels useless or as if their character's actions have no significance. I personally played a character whose main contribution to the end boss fight consisted of shopping for consumable items, and another who was left behind when the end boss and another party member ethereal jaunted away to have a several round one-on-one duel. Though this didn't spoil otherwise enjoyable games it certainly detracted from those encounters.
If your player is OK with just not using the scrolls, and feels he is still contributing to the game, then that's OK, but if not then figure something else out.
Recently, we have been playing a certain Pathfinder module that grants a +1 to WIS or CHA after a certain event. I am playing a fighter in that game and those ability scores were useless to me from a pure stats point of view. However, my character's wisdom went from a 10 to an 11, and I started to role-play her being a little bit more cautious (wiser).
Repeatedly, or only after one specific event? One stat boost once is not a huge power increase, so it's not that big a deal if some characters find it more useful than others.
Levels, plural, in a class is a big power boost.