Nope, they've always been an independently owned company. They just have a good relationship with DC. DC publishes and distributes the Milestone comics, but they could take their characters to any company they want.
If they decided they wanted to take the Milestone characters to Marvel, Image, or even Valiant they could.
Before he died Dwayne was working with DC and he had publicly complained that he felt he wasted money on lawyers trying to work out a new deal with DC only for them only show interest in Static and let the other characters fall to the wayside. Part of why that last Static series flopped and was canceled was because DC started making changes to the characters without permission from anybody at Milestone.
They supposedly worked out a new publishing deal with DC sometime last year, but nothing has come of it.
*edit*
This is from 2015
DC ENTERTAINMENT ANNOUNCES THE RETURN OF THE MILESTONE UNIVERSE WITH THE CREATION OF ALL-NEW ‘EARTH-M’
This feels like what happened last time. DC announced they were going to publish some Milestone stuff and then we don't see or hear anything for nearly 3 years because of a bunch of legal red tape.