That really is a tough call for a player. Obviously in a regional or higher level tournament you have to hold a player accountable for an illegal deck. At that level they should know the ban list and all of the other rules as for what's an illegal deck or not.
On a local level though the line greys a bit. You don't want to discourage a new player and get them upset. I can understand it if you're playing someone completely new in the first round and they activate their second
Pot of Greed and you whisper, "Hey, I don't want to see you lose this match because you have an illegal deck,
Pot of Greed is limited to 1 per deck my friend. Why don't you just draw a new card and fix your deck in between rounds and we'll call it cool alright?" That's commendable on your part and a very giving thing to do with their best interest in mind.
The problem with the above scenario though is it's a bit more involved that it first appears. First, how is this person going to fix their deck? They've already turned in a deck sheet, if they take a card out and they only have 40 cards in their deck they could take a card out of their side deck....if they have one, and then they'd still have an illegal deck with a side deck count at 14. Their deck sheet would be off as well. If they pull a card from their binder to replace the second
Pot of Greed then they still have an illegal deck sheet. Secondly, if it isn't first round they player previous players with an illegal deck possibly making their chances better to win and those players may have lost because this person is playing 2 or 3
Pot of Greeds, that's not fair either.
If this person would change their deck and later have a deck check, and then the judge points out the error and this person says, "Well Yugi over there just told me to switch the card out." then you're in a heap of trouble with the judge.
I really can appreciate the compassion and spirit with which the statement made about not wanting to win by technicallity was made. I think, however, in the long run it possibly won't benefit either your opponent and it may reflect poorly on you (though obviously your spirit of fair play and intention was good) At worst this person would take a match loss and move on. I think most of us have taken one on the chin at some point along the line that way. We learn best from our mistakes.