There's one decisive problem with not destroying capships at all times. The reason is it's impractical to sacrifice valuable resources on capture opperations not essential to the mission objective.
Let's guage the risk associated with known shiptypes. Transports are the easiest vessels to capture and are similar in nature to ships under repair because they're slow, lightly armed and armored, and have minimal crew complements. Assuming a shuttle full of Marines can dock with with transport, doing so will leave it vulnerable to attack. Boarders don't have clear run of the ship once aboard, either. They can meet substantial resistance from even a small crew, they can run into traps, force-fields, bulkheads, all of which can isolate and contain them. If they're well trained and not too well outnumbered, they could seize the vessel. The next question is can they get the ship running again and opperate the ship effectively? Maybe, but probably not. If a fighter escort is supporting the opperation, it cannot participate in protecting its mothership for a great deal of time because of the shuttle's low speed. They have what can be a very tough job of protecting two defenseless ships from enemy attackers. Even if all goes well, you've expended valuable time and resources on a gamble that could blow up in your face with an auto-destruct sequence. While ships undeconstruction or repair offer less resistance, chances of gaining something worthwhile out of the opperation are minimal, especially if the engines aren't installed! Missions of this kind could enjoy some success with significant loss of resources with a well-executed plan.
Small warships would be more difficult for several reasons. Ships of this type are often fast and are capable of concentrating firepower effectively. These are military vessels, hence they are far more likely to carry trained warriors capable of repelling armed invaders. Military ships are more likely to destroy themselves to prevent capture because they don't have valuable cargo to preserve. Successfully capturing these vessels is unlikely without well equipped, fast-acting personnel.
Medium-to-large warships are by far the least promissing prospects for capture. Unless you can totally shut down the ship's defenses without losing your whole force in the process, odds of capture with a small boarding party are almost negligable. Seizing and controlling what would be a large area with a small force would be difficult at best. It's not like Landing Craft of teleportation devices allowing troops into sensitive areas directly, troops have to fight their way from the outer hull.
What I'm saying is full-scale capture opperations against a heavily armed, mobile force may cost as many resources as it will likely gain. It's far quicker to deploy a few medium-to-low cost weapons to destroy enemy forces than risk finite resources for extended periods of time on what could be a very large front.
---> [choking sounds]
