Put aside the FTC situation - that's out of the Phillies control. There is no way that a Stanton plus Stroman deal, for example, strips the farm.
Even if Stanton costs you Velasquez, Pivetta and Quinn, for example, and Stroman or equivalent costs you Cesar, Williams, Kilome and Anderson, for example, you still have this on the farm for pitching and OF:
P: Sixto, Medina, JoJo, Seranthony, Suarez, El Garcia, Mills, Howard - not to mention Lively, Thompson, Leiter, Eflin, Eickhoff
OF: Stanton, Altherr, Odubel, Tocci, Haseley, Randolph, Moniak, Ortiz, even Cozens
As for free agents, I'm with you...if you knew you could get them. However, could easily see Otani, Darvish, Harper, Machado all signing with the Dodger/Yanks/Red Sox/Cubs. Also will have to compete with the next tier of Nats/Rangers/Cards/Giants/Angels. Not so easy.
Not to mention that the new free-agent contracts are likely to be pretty expensive as well – JD Martinez is rumored to be asking for a $200 million contract. Harper/Machado could easily be $35m for 10 yrs - Stanton may not look that much riskier compared to that.