The idea or notion that the Phillies were in the right and the kid and his advisor(agent) were in the wrong is somewhat incomplete and hypocritical when you consider the entire situation.
I think pretty much every baseball team in the majors, every baseball team in college, every agent, every NCAA baseball official pretty much knows that the 'advisors' for amateur players when drafted are agents. Once the player signs a deal that 'advisor' usually gets the 4% or so agent cut as the advisor becomes the players agent.
Hundreds of players every draft likely use their 'advisor' in the exact same manner as this player did, most of those players do sign contracts, some do not... but the MLB teams don't "rat them out" and try to punish the player.
Now if you could look at this situation and say the Phillies reported something that they and every MLB team knows goes on just because they felt "slighted/jerked around" by the 'advisor' of the player or the player himself that's one thing. You could say while teams let the rules be broke, the rule was broke.
But the Phillies are not angels in this negotiation. The Phillies also broke MLB draft rules by doing something every other MLB team also does and which gets 'overlooked' in a similar manner to the player's advisor being in all but name an agent.
The Phillies negotiated/discussed bonuses with players prior to drafting them. By the letter of the law for the draft rules in MLB that is something which teams are not allowed to do. It's something which under the new CBA happens even more than it did in the old days. The reason being in the new CBA you have a draft pool that you can't exceed for the first 10 rounds or else you can receive financial penalties and if you exceed it by 5% or more start losing subsequent draft picks.
To counter this new draft pool teams have realized that if they draft a junior or senior NCAA player in rounds 5 thru 10 and get that player to agree to sign for a bonus that is 'underslot' then the team can apply that savings to "tougher signs" and exceed slot bonuses. Let's say your 2nd round pick has a slot value of $1.5m, but the kid wants $2.0m to sign. By shedding a few $100,000 off signing bonuses to your 7th/8th/9th round picks you can make up that difference.
The Phillies are basically pulling a pot calling the kettle black here in that they are mad because the kid and his agent didn't follow-thru on the agreed bonus when that pre-draft agreement is itself against the MLB rules.