There are three fan edits that incorporate deleted scenes, however they make many other changes as well and do not necessarily use all the new material available.
Here they are with brief synopsis:
- Prometheus: Giftbearer (February 2013)
Incorporated deleted, alternate and supplementary footage and made
numerous edits to original scenes to strengthen story, clarify
character motivation, and address some often-mentioned issues viewers
had with the original theatrical release.
- Prometheus – Special Edition (May 2013)
Prometheus SE cuts out a lot of the unnecessary humor, dialog and
scene's, building stronger, smarter characters. Removing many plot
holes with the story and just general things that have issues. Such as
Fifield getting lost in the structure, running in a straight line away
from a rolling space craft. Deleted scene's or certain shots from the
deleted footage was re-integrated back into the movie by either using
several shots to change certain scene's or by adding a whole new scene
to the film. All new material was color corrected, scored, sfx added
and leveled to appropriate audio levels.
- Prometheus Unbound (November 2013)
Highlights of the edit include the following:
The opening sequence with the first Engineer has been all but replaced
with the opening Ted Talk followed by a montage courtesy of Tree of
Life. Holloway's douchy-ness has been seriously reduced, Shaw no
longer makes faith-based decisions and Vickes' bitchiness has been
mostly removed. No more exploding head and the attack on Fifield and
Milburn has less idiocy on their part. The ship falls on Vickes
without giving her time enough to "just make a right turn."
All three are available on fanedit.info. Note that the legality of sharing/downloading fan edits is questionable. You can find more info on that on the above-linked Wikipedia page. There is a download guide on Reddit.