You are "forced" to do quite a lot of things in all RTS games. Building troops, securing resources of all kinds etc...
To take a game of "comparable" scale I'll go with supreme commander (1 or 2, same deal in that compartment). In order to protect your base from lategame nuking you are forced to either build nuke defense structures or rush to the location of the nuke silo and blow it to bits.
In smaller scale games there is a smilar problem, let's take a look at C&C: In order to stop a superweapon from wrecking a large portion of your base you need to get it killed before the timer runs out.
I could even point out quite e niche game: In Earth 2150 you were forced to protect your base from the various superweapons of the various factions with completely different means (anti-missile platforms only protected against missiles, they didn't block plasma barrages or lightning storms). Some superweapons could even be planted on vehicles, making them incredibly hard to track.
Btw, three hours are quite a long time in Sins, you can conquer whole empires in that time. Placing a starbase on your planets early-on will give you other beenfits, too, so it's not that bad a deal (you know, tradeports, factories, culture facilites and the like). You actually miss out some very nifty advantages if you leave all your planets "naked".
The one thing I agree on is that there is very little preperation time in Sins, from my experience you only get informed about the superweapon when it is completed, seconds before the first shot. Maybe a longer construction period and an announcement upon placing the thing or the constructor starting his work may be a help.
Btw, all races can reduce the impact of the Novalith. The Advent bombing protection research reduces the damage from 3500 to 2950, the vasari have a similar research if I recall correctly, and the TEC can use their planetary shield to reduce it to something around 750 ~ 850.