Hello avivz..
If a heaviest subtree determines current network head, then two things will be possible with a 50% attacker that aren't currently possible now:
1) You can actually strip off head and the chain length can move backwards. (This includes rewinding back past a difficulty retarget, which is currently impossible.[1])
2) You can create a scenario where two mining factions create divergent forks which simply add to their own subtree weight, and the main chain length goes ~nowhere.
With the way bitcoin is currently built, neither of these two possibilities is.. er.. possible. All 50% attacks must, even though they rewrite history, move head
forwards.
Whether this has any meaning in terms of risk to bitcoin users I suppose is another matter than the point of my post. Did you address these possibilities in your paper? I ask because I read a good chunk of it, but not all of it, for which I apologise. I am extremely happy to see academic work being done on bitcoin.
At the very least, I'd like to encourage you (as I am a random internet nobody

to create an experimental fork with this idea built in as a testnet alternative.
Hrm.. I suppose in terms of user software, all current infrastructure which makes assumptions about the current rules would be exposed to risk by a switch to ghost-enabled bitcoind..
[1] maaku pointed out people may be confused with my terminology: a replacement of work can "rewind" a chain in the sense that the history is substituted with another history of greater work in a non-GHOST mainline: "Rewinding" in the sense I mean it here is to
strip off the numerical topmost block so that mainline head is actually prior to the retarget point: using GHOST orphans it is possible to erase the retarget and make it historically as though it never happened.
I don't think I understood your first point. I'll be happy if you could elaborate: are you referring to something regarding the re-targeting moment?
As for number 2: it seems like if there are two factions insisting on building split subtrees then one of these trees eventually grows larger than the other (even if they are evenly matched! See our analysis of "collapse" in the paper for this exact scenario) in this case one of those factions is not abiding by the protocol if it doesn't switch to the other tree -- this is a 50% attacker.