It's implied that Gallifreyan troops have decently powerful protections of some sort. For context, a Rutan (in actuality, a Sontaran-Rutan hybrid created by the Sontarans to bait the Rutans' destruction) infiltrated a Battle TARDIS with its abilities, and slaughtered the crew of a Time Lord space station that encroached on their territory. Normally, such a station guard would've been 'clearly capable of dispatching a mere Rutan', but the crew was limited due to the station being near the frontline, and the Rutan was believed to have acquired shielding and weaponry from the crew of the Battle TARDIS.
The Time Lords, at this point, were stretched too thin to potentially fight both the Daleks and the Rutans, and didn't want to encourage such behaviour from other 'minor' races, so the Time Lords were prepared to straight up erase Ruta III from all of space-time with a Battle TARDIS fleet. Similarly, the Rutans couldn't afford confronting even the Time Lords' diminished resources and the Sontarans simultaneously.
The Time War is said to take place 'beyond reality'.
The Time Lords and Sontarans have diplomatic relations of some sort, and the Time Lords even attempted to recruit them into an alliance. The Sontarans claim this is because Gallifrey don't have much experience with this kind of war, whereas the Daleks and Sontarans have been doing so for millennia.
A Sontaran Commander sees a TARDIS (specifically The Doctor's TARDIS) heading towards Sontar in the Vortex, and orders his adjunct to shoot it down. Normally, I'd say this is just Sontaran foolhardiness and ego, but the context and manner in which it's said leads me to believe the threat was at least somewhat serious. Plus, a Sontaran General later reiterates that The Doctor would've been fried before landing.
For reference, the planet Sontar, by this point, is reserved entirely for machinery of war (presumably including cloning berths), meaning that any diplomacy takes place on the battle fleet. So, the Commander could've been referring to his ship, the fleet in orbit, the defences of Sontar, or all of the above. Given what I mention below about the Rutan fleet, I think it's all of the above.
Sontaran genomes are normally incompatible with Rutan shapeshifting and hybridisation, and attempts to gather their DNA is extremely difficult due to Sontaran security.
Falling through the Vortex is maddening enough to 'break' Sontaran/Rutan minds (it makes them less insane, if anything).
Throughout the story, The Doctor and Skole (a Sontaran who was intertwined in these events due to his past with The Doctor) had visions of the universe being destroyed and time collapsing.
The erasure of Ruta III would create a grandfather paradox because if the Rutans never existed to attack the station, then the whole sequence of events that would've lead to their erasure wouldn't have existed either. The Time Lords planned to preserve the chronology by trapping the planet's destruction in an anomaly cage (explicitly
The Heretic's design), removing cause but keeping effect.
However, this would've failed and caused the entire universe to collapse because the events of the story were also caught up in a bootstrap paradox (specifically, Sontarans in the future created Sontaran-Rutan hybrids that were lost in time and appeared at the Giant's Causeway, so the Rutans could create Rutan-Sontaran hybrids in the past, meaning that the Sontarans in the present could collect the Rutan-Sontaran hybrids that appeared at the Giant's Causeway), and the Anomaly Cage (if not all Time Lord technology) isn't designed to deal with two paradoxes that occur in separate time frames.
For reference, bootstrap paradoxes are very difficult to create, but it's a 'standard Wednesday' in the Time War. This is supported by The War Doctor casually being able to break the First Law of Time for the same reason in
Exit Strategy.
It's implied that a war with the Time Lords (even during the Time War) would go very badly for the Sontarans.
Rutan ships can't break through TARDIS forcefields, but they do prevent the Time Lord fleet from dropping the 'planet-killer' (the same term used for the device in
The Last Days of Freme, but presumably far more powerful) on Ruta III because the warships are forced to waste time (at least a matter of minutes) on obliterating the Rutans.
For reference, the Time Lords probably didn't just bombard the planet because of the circumstances involved; the planet-killer is a volatile (to the point where it'd detonate during Vortex transit), dimensionally transcendental (small enough on the outside to be held in The Doctor's hand) explosive device that's specially linked to drop the Anomaly Cage on Ruta III before detonating.
TARDIS forcefields stop other TARDISes from materialising inside them.
Sontarans are particularly non-time sensitive.
The Doctor's temporal grace is functional.
When The Doctor uses the planet-killer on the hybrids, it consigns everything in
Sontarans vs Rutans to a somewhat distinct timeline due to the fact that it erased the crew from history (including Skole), but the events still happened in the normal timeline.