Remove the Cylon virus from the picture. Instead the Cylons launch an all out offensive against the colonies. Given what we know of the respective fleets and technologies, who would win?
The way I see it :
Have superior technology in many fields. Vastly better navigation; given what we've seen, it's likely a Cylon fleet could jump clear across most of Colonial space and right into orbit with complete surprise (which indeed they did do). They can operate complex interdependent computer systems safely, likely giving them a better ability to co-ordinate. Seem to have far superior missile technology to the Colonial fleet, or at least they choose to be reliant on missiles far more than the colonials do. I've always opined that this gives them an advantage at long range in that a missile can maneuver to hit the target when a shell cannot.
Their chief weapon is surprise; since they launch a sneak attack they can do so with their whole fleet, when the Colonials would likely only have 1/3 of their own fleet combat ready at any given time (that's assuming they followed something approximating present day naval practice). On the other hand they would face whatever fixed defences the Colonies may have had, if any.
Cylon crews can, presumably, fight 24/7 without rest, at least until maintenance is needed.
On the downside; the Cylon motherships seem to rely on missiles and fighters to keep enemy hostiles out of range. They seem to entirely lack point defence, and if heavy hits are inflicted they seem quite vulnerable to them. This last stems at least partly from poor basic design; six long thin arms, all of which can be sheared off by one or two hits at any point along their length, and a central joint/hinge which if hit can lead to an "unrequested separation" of the ship.
Seem to be rather complacent regarding the Cylons in the miniseries, which must make one wonder just how prepared they were for a major attack. We've seen only two high ranking officers; Adama and Caine. Both seemed to be very capable in terms of combat, and both seemed to be aggressive warriors, unafraid to push for victory. If this is typical, then the fleet seems in good hands.
Battlestars are, perhaps, somewhat lacking in advanced technology compared to the Cylons. But some of the mismatch is negated by the nature of the surprise attack; for example whilst the Cylon's superior navigation may get them into orbit undetected, once there that advantage counts for little (unless they want to disengage and retreat). We see from The Plan that the Colonials do indeed have time to get Battlestars into the field and mount a defence, so whatever advantage was gained, surprise was not absolute or overwhelming.
Perhaps critically, the Cylons seem to have erred bigtime in their apparent doctrine of hanging back and saturating with missiles. Colonial point defence relies on massive saturation with unguided cannon, and this seems to be highly effective; Galactica stood against not one but several base ships in the miniseries, albeit briefly. Most tellingly, the idea of hanging back never seems to work. Whenever the Battlestars go for it, they have been able to get in close to the base ships and strike at them directly.
Unlike Cylon ships, Battlestars are designed to take damage and seem well capable of doing just that. They have withstood nuclear missile strikes - sometimes several of them in the case of the Pegasus - and remained fully combat capable. To judge by Pegasus, if it gets in close a modern Battlestar is more than capable of taking on and defeating a base ship one on one, and indeed seems capable of taking on two, and of at least putting up a good fight against three. If that is even close to representative of Battlestars in general, then even 30 or 40 Battlestars getting into the fight would make a truly formidable force, well able to stand against 100+ Cylon base ships - and that's without considering whatever fixed defences might be available.
Personally, I have to give this one to the Colonials. Battlestars are cruder, perhaps, but they are just too tough and too heavily armed and too numerous for the Cylons to take them out.
And ultimately... well if the Cylons could have won a straightforward war, why take the risk of launching the whole covert virus thing in the first place? It was after all a highly risky strategy; had it gone wrong you've committed an overt act of war, put the Colonies on full alert, revealed the existence of humanoid Cylons, and gained nothing from it. I begins to see the sneak attack as almost an act of desperation for an enemy who could win no other way.
Give a man a fire, and you keep him warm for a day. SET a man on fire, and you will keep him warm for the rest of his life...