Can ATC separate IFR traffic in class A airspace from VFR traffic in class E?
Keep in mind that ATC only separates IFR traffic from other IFR traffic. So they would not provide separation from any VFR traffic no matter what the airspace (with the exception of Class B).

AIM 4−4−11. IFR Separation Standards


  b. Separation will be provided between all aircraft operating on IFR
  flight plans except during that part of the flight (outside Class B
  airspace or a TRSA) being conducted on a VFR−on−top/VFR conditions
  clearance. Under these conditions, ATC may issue traffic advisories,
  but it is the sole responsibility of the pilot to be vigilant so as to
  see and avoid other aircraft.