The missile cruiser, known as the EAC Soter, will not replace either cruiser from classic Inferno. Instead it will feature as a defensive/support ship by firing long-range missiles behind the front lines. It will not carry the iconic EA silver beam cannon but will carry long-range mass drivers, dealing pain and death to smaller (cruiser and smaller support vessels), not unlike the Vaygr Trinity Cannon from HW2.
EA beam cannon technology (or "flux cannons" as I like to call them) is quite different from those used by the GTVA, since they have no Vasudan-influenced technology. Instead it is a proprietary design based off of the Lucifer's flux cannons from the wreckage and perfected over the course of INFA. It is supposed to be weaker on a per-shot basis but use less power and thus can fire faster (currently not balanced).
BTW, although we take a lot of influence (a good thing) from the Homeworld series (and other sources) when designing our ships, we do not rip any ships directly from the game and claim it as our own (something one should never do). All meshes are either redesigned from scratch or modified for FS2 and used with permission from the donor (e.g. - the EAD Basileus). Nevertheless, we never fail to give credit to where it's due.
-R