His exact words are “as for the suit, I think you’ve earned it.” He never says he wouldn’t take it temporarily. All he implies is that Gordon deserves the suit in his possession, which Gordon does end up having anyway. He never lied about anything here.
Honestly you’re looking too deeply into this. It’s completely not an issue.
But not permanently like most of the other weapons. He relocates the suit so that it can be upgraded but you are still in possession of the suit much like I’m still in possession of my computer at home even if I’m taking a vacation out of the country.
I think it’s the best to be as it is now tbh (also quite some off-topic, so let’s get back on track).
If he’d say something like ,As for the suit… I think you’ve earned it, but I’ll take care of it, until the time comes round again, (this also slightly resembles his speech from the end of HL2), he’d be too explicit that wouldn’t be the G-Man we all know and love (I hope 
).
He’s, by his very nature, cryptic and very mysterious. I think it should be how it’s now, it’s the best. I agree with danielsangeo’s point of view regarding this matter:
“As for the suit…well…you’re not going to need it for a while. Oh, don’t worry, I’ll make sure it finds its way into…friendly hands.”
Founded in 2004, Leakfree.org became one of the first online communities dedicated to Valve’s Source engine development. It is more famously known for the formation of Black Mesa: Source under the 'Leakfree Modification Team' handle in September 2004.