Dragon 2 (Crew Dragon) has two separate types of engines: the powerful SuperDraco thrusters (currently planned only for use in launch escape) and the much smaller Draco thrusters used for attitude control and orbital adjustment (including de-orbit). Draco thrusters are also used on Dragon 1.
As for why the SuperDracos are still integrated with the capsule instead of being on a removable component, the most obvious answer to me is that the capsule is already reusable, the SuperDracos are presumably expensive to manufacture, and anywhere else they were mounted would need to be made reusable at considerable effort and expense or else the SuperDracos would need to be expended on each flight. For example, the SuperDracos are not mounted on the spacecraft trunk (the "cylindrical thing equipped with fins under Dragon", which mostly holds the solar panels and unpressurized cargo) because the trunk is not reusable - it is jettisoned before re-entry (it needs to be; it covers the heat shield) and burns up in the atmosphere - so mounting the SuperDracos on it would require expending them or making the whole trunk recoverable somehow. Similarly, designing a reusable launch escape tower would be quite a trick; the tower would block an important part of the capsule (its docking hatch) so it would have to be jettisoned in flight, and recovering things jettisoned in flight is difficult.
Finally, remember that this capsule has been in design for a long time. Making a major change to one of the critical safety features - the launch abort system - is not something you do to a spacecraft that is already behind schedule without a very good reason. It would need to not just be a better design, but to be a sufficiently better design to justify a massive amount of additional work. That work is expensive (SpaceX is building the Dragons on a fixed-price contract, so they eat any cost overruns), risks pissing off the customer (NASA, who - although they've largely embraced SpaceX for routine ISS missions - are still deciding who will receive some quite lucrative contracts for lunar missions, etc.), and risks losing both corporate and national pride/prestige (due to Boeing sending astronauts to the ISS first, and the USA being forced to buy more flights from Russia, respectively)
This next part is pure speculation!
It also occurs to me that the SuperDracos, being mounted to the capsule, could be used for emergency landing support. The capsule is not designed to land on solid ground (no legs or airbags) but, in an emergency, the combination of its parachutes and SuperDracos could almost certainly make a dry landing survivable (for the crew, at least; the capsule might never fly again). Alternatively, in the case of a partial parachute failure during an otherwise-normal landing, it's possible the SuperDracos could provide a braking/landing burn prior to splashdown, cushioning the impact (although then you get seawater meeting hot rocket nozzles which would almost certainly damage the SuperDracos, but they're already isolated from the rest of the capsule; the people and/or cargo would probably survive).
Another possibility is that the SuperDracos could be used as a backup propulsion system for in-orbit maneuvering. Although the Draco thrusters are both redundant and highly reliable, when you're dealing with people's lives, it can be beneficial to have a little extra redundancy. While the SuperDraco system is designed for short, powerful burns, it's quite throttleable - SpaceX likes to show a video of it being used for hovering the capsule, on their webcasts - and could theoretically be used to de-orbit the capsule if the main propulsion failed for some reason.