The Whirlwind was the long range bombardment, sure, but it had a decent anti-tank role as well. There were no rules for aircraft yet, but in the fluff it was said a few times the Whirlwind was the also the Space Marines anti-aircraft platform, which makes perfect sense. Space Marines have some of the best tech of the Imperium, so a AFV that packed multi-purpose missiles fits them perfectly.
So what to do? House Rule time.
The Space Marines clearly have the tech for a missile launcher that has different ammo types. The basic Infantry Missile Launcher, and the Typhoon Missile launcher do this well. So should the Whirlwind, just bigger and better. Here in my simple proposal:
The Whirlwind is armed with a Vengeance Missile Launcher. Like the Typhoon launcher, it can be fired one of several different ways each turn.
Frag warhead: Range:12"-72" Str:5, AP:4, Large blast, Barrage 2
Krak warhead: Range: 48" Str:8, AP:3, Heavy 2
May add one addition missile type:
Incendiary warhead, Range:12"-72" Str:4, AP:5, Large blast, Barrage 2, ignores cover, +15 points
Flakk Missile, Range: 48" Str:7, AP2, Skyfire 2, +20 points
I think this goes a long way to making the Whirlwind a viable weapon again. It is not as good as any dedicated platform like the Basilisk or Hunter, but it can do it all, and that is what the Marines need.
The Emperor Protects
And Rains Death Upon the Heritics