For a character to be Good they must actually act Good and do Good deeds regularly, because they choose to be a Good person, and not simply to "top up" their align-o-meter.
In D&D, alignments are Cosmic Absolutes, not simply moral judgements of the mortal races. Regardless of the how a given people act or think, there are Greater Powers out there in the metaverse which exemplify the actions of Good, Lawful, Chaotic, or Evil. And even then, the definitions of these alignments are beyond the nature of those beings; the definitions are stitched into the nature of the metaverse itself.
If this Cler/Malc commits Evil acts regularly, they are becoming Evil.
Committing an act of Good to "balance it out" will do no such thing.
Option 1: Committing an act purely to adjust their alignment is an inherently 'deceptive' act. This is Chaotic behavior. It will not make you any more Good than taking no action at all, and it will over time shift you towards Chaotic.
Option 2: Committing an act purely to adjust their alignment is an inherently 'false' act. This act, by the nature of not being truly invested in it, has no meaning. It will not adjust your alignment in any significant manner.
In either case, one can argue that "A Good act is inherently Good" which is not untrue. But the argument also applies that "The act was committed for reasons that are not Good" - eg, to cover up their true nature. At best, they might receive a miniscule bump towards Good, but weighed against willingly and freely committing Evil acts, the most this could do is slow their progress towards evil. They would need to commit multitudes of these Good acts to ever come close to balancing out, and if they are committing so many Good acts, this would change their core nature towards Good over time. Because alignment is an absolute thing in D&D, "you are how you act, and you act how you are."
Looking at it from the perspective of players, it feels like he is 'gaming' the alignment system, and brings up the inevitable question of "If X can do it, why can't I? I want to be a Lawful Good murderhobo whose Evil actions simply don't count too!"
But with all of that said, there's still an easy solution to preventing them from short-circuiting the adventure!
(Ok, so i get it; this was a year ago, and this particular campaign is probably long past it. But as always, advice for people who may encounter it in the future.)
Another thing that is in D&D, especially 3.5e, is the near omnipresence of magic items. Even by 2nd level a typical party has probably picked up a trinket or two, and by the time they are approaching 10th level many players are more "blinged out" than a flashy rap star.
So why wouldn't someone trying to disguise their evil nature have some little trinket or spell of their own that causes a Detect Alignment spell to read falsely? Misrepresent Alignment is already a 3rd level Cleric spell (from Races of Eberron). Lasting 1h/level, it seems like it could be used as just another step in your morning routine - get dressed, brush your teeth, comb your hair, fudge your alignment, and now you're ready for a day on the town!
At 10th level, they could even craft an item that automatically does it for them. This could lead to the "Aha! This is how he's done it for all these years!" moment after the climactic battle. After such intense scrutiny (and probably a battery of Detect Alignment spells from every investigating mage) the little amulet finally breaks, falling off his neck for someone to find and recognize.
Side Points to consider:
Detect Alignment spells might be considered either taboo, or outright forbidden as part of the investigation.
It might be considered an intrusion of privacy to just snoop around blindly with Detect Alignment spells, and have social repercussions. "Oi! Don'chu wave yer Eyes Of Snoopin' at ME you nosy basterd! -purse smack-"
It might also be forbidden as part of a "Fair and Unbiased Investigation". This is highly dependent on how formalized the investigators are, of course, but perhaps a long string of "He's Evil, lock him up boys!" followed by clear and obvious proof that they had no connection at all to the crime resulted in legislation that prevents Investigators from using that ability as any sort of evidence.
This is likely related to...
Evil does not (always) mean cackling madmen out to conquer or destroy the world. Evil people also live in the city.
Maybe the bar bouncer who enjoys getting too rough when tossing rowdy patrons out. Maybe the dock worker who's always got some kind of deal running on the side for himself. Or the politician who does the same thing. The Lawful Evil priests of the local temple of the Death God who commit human sacrifice each month, but only of willingly chosen volunteers of their cult. Etc..
Neither Evil nor Chaotic people are inherently unable to live within a city. In fact of the two, Chaotic is more likely to have trouble with it due to the general disposition towards Law and Order within a well run city.