Be advised, that my No.2 method will have some slight problems. If you wait to destruct both ships (or even just the transport since it'd be illogical for the Science Cruiser to blow up first) too late, the speed of the transport will cause it to bounce off the hull and then explode, which won't look right. You can avoid that by causing the transport to explode earlier, but then it will seem to start blowing up before it makes contact with the science cruiser. One solution does come to mind, however its somewhat complicated and definitely requires SCP. First, using the associated sexp, give the transport with a "vaporize" flag. That will cause it to desintigrate rather than go through the standard death-roll. This will eliminate any bounce, since there won't be time. Now, this will IIRC, remove the explosion of the transport, but there is a sexp to give an explosion at a specific location, which can be timed to the vaporization of the transport, followed by the subsequent death-roll and destruction of the science cruiser. This will require you to know exactly where the science cruiser will be at the time of the explosion. If you have it stop at a waypoint prior to the impact, remember that ships may take a bit of space to decelerate after reaching the waypoint, so trial and error will be needed to get the location correct.
I told you it was complicated.
Later!