Isn't it the business of the judiciary branch (read: courts) to decide if something is unconstitutional or not? What business does the Congress have in this to begin with, unless they amend the constitution to allow the discrimination against openly homosexuals?
Seriously guys, your government should really keep the executive, legislative and judiciary branches separate... 
Alright, let me break it down.
1) A Federal District court found DADT unconstitutional and ordered an injunction for the military to stop discharging homosexuals.
2) The Department of Justice essentially halted the injunction, which means there's not really an option in the courts to repeal it based on it's unconstitutionality.
3) Congress, on the other hand, can repeal it, since it was an act of Congress that first implemented DADT. They have the power to repeal one of their own pieces of legislation.
So yeah, a court DID find it unconstitutional, but a higher court essentially blocked the ruling. That's why Congress is necessary.
It's not really an issue of the branches stepping into each other's territories, it's just another viable option where one fell apart.