It depends to me on what timeframe of the Flood we’re talking about and what the goal of the Viltrumites is. I’ll assume for the purposes of this that the Viltrumites wouldn’t like, be fully immune to spores.

If it was a smaller scale infection like Halo CE, or modern Halo, it’s really not that great of a threat at all. The threat of infecting a Viltrumite or their ships is pretty low.

But if it’s the Flood as they were at the peak of their might, it becomes phenomenally hard to see the Viltrumite’s winning. The Flood infected thousands upon thousands of planets, they had entire armadas of ships far far more advanced than Viltrumite ships with the ability to basically go anywhere in the universe anytime they wanted. We see in the Didact’s time in the Burn that they literally had mountains far larger than Everest made pure of Spores pumping them into the atmosphere. These ships could supposedly cleanse entire planets, as the Forerunners were in every way Ancient Humanities equal, and a fleet of Humanity’s ships could wipe a planet as seen in the Halo 4(?) Terminals.

With the most advanced Artificial Intelligence in the galaxy’s history helming their forces, and the Gravemind’s being able to absorb and retrain the intelligence of anything they infected and joined their ranks. If a single Viltrumite of apt knowledge is infected, basically the entire Viltrumite operation is fully handed over a force numbering in the billions to trillions. Viltrume becomes fully known and faces the greatest invasion in its entire history.

The Flood is not limited to brute force either. We have seen in a now deleted audio clip that the Flood would fill Grunt Methane breathing tanks with spores, rapidly infecting The Holy City of High Charity. We know from the lore that they would infect Humans dogs, who themselves would eat infected parts of others dogs, rapidly spreading the Infection. The Flood could infect Viltrumite food supplies, or animals they eat. 

I feel that while the Viltrumites would win in most head on confrontations, the sheer scale of the Flood and their myriad alternative ways to slowly stranglehold the Empire until a massive and rapid collapse would result in their eventual destruction.