This answer to my previous question made me thinking -- why Voyager wasn't able to travel back in time, in the end of "Future's End" episode, without assistance of Capt. Braxton's ship / 29th century technology / created time rift, if in "Star Trek: First Contact" TNG crew managed to return back to "their" time without assistance from the Borg or anyone else?
In Star Trek: First Contact, the Enterprise used the existing time-rift created by the Borg to return to their own time.
Excluding a couple of "early episode madness" episodes from TOS, the only other instances we see of time travel being initiated by a crew from the 22nd, 23rd and 24th Century are various accidents and the single instance of the Klingon vessel from Star Trek IV which was notably crewed by Spock who was (apparently) keeping the secret of time travel to himself.
Janeway really had no choice. Alternate Braxton could have enforced his direction to Janeway if she chose not to comply. This was not about having the means, but having to comply with someone who can back up their request with lethal force.