The problems with alts and the related problem of initial alliances setting the order of fortress kills is never going to be easy to fix! Various solutions to one or other have been proffered in the past, but all have a downside.
One solution, not a new offering, that I think may assist is that anyone with a badge on the world can't shoot or inject the virus again. This will discourage top players moving into the 2nd and 3rd (etc) alliances to kill the fortress but doesn't prevent them from assisting other players in getting to the centre.
Alts are a different problem and would only be solved by use of some limiting system. One whereby more than one player can't log in from the same machine (note, not the same IP/location), maybe within a set time period of 12h or 14h may be suitable. Of course, it may not be technically possible within a browser game. EA controls the login process so they're the ones that would need to implement it.