Smaller ships, such as frigates or destroyers are a more appropriate option for small kill-teams. Imperial and space marine frigates and destroyers are can be found ranging and patroling away from large fleets. Imperial ships usually do this in squadrons while space marine frigates, when operating seperate from a larger combined fleet, tend to work as singular ships patroling sectors and providing support to planets who need their help or whom the chapter has sworn treaties or oaths.
The space marine frigates will rarely have more than a single squad of Astartes on board, when they do it is likely no more than a few more as those ships aren't designed for large Astartes capacity. Besides, 10 Astartes is more than enough for general picket, patrol, and many assault missions. Space Marine ships are designed with the most advanced tech the ad mech have and are usually very automated, requiring a very small crew of chapter serfs to operate compared to imperial navy ships.
Navy frigates and destroyers usually provide the same picket and patrol missions as the Astartes ships but usually do so in squadrons. Under special circumstances, a fleet will dispatch single ships for certain missions. Being comandeered by Inquisition of Deathwatch would be such a special circumstance. But these ships aren't as big or robust as larger ships, they may get you into a system but they aren't going to brave 2 orbitals, 3 cruisers, and 5 squadrons of enemy frigates to provide the kill-team combat support after they get on planet. They are going to find a nice large asteroid or something to hide behind or warp out while waiting for the kill-team to get back, or returning at a pre-arranged time.