I feel all of your pain and then some. I have completed all there is to complete on Havarl including the final mission twice (reloaded to see if it would help.) I cannot leave the planet. Hold down the "Y" button and the meter fills but does not complete. The sad part is that I have completed two other planets already so I am currently level 33. That is a lot of time to even think about restarting this game....Sheppard wouldn't do this to us.
*Update - Mine was also having the problem of the "Extract to Tempest" disappearing in two seconds. I picked the best load out station that I could blink to in time and was able to use the "Extract to Tempest." Maybe you guys can try that method.