The lines themelves are plastic, what they are telling you is that the unions that hold the lines to the pump are corroded. Once the unit is removed from the cavity it lives in and pulled back into the trunk you should be able to use a brass wire brush to clean the unions up without disconnecting them. If the motor part of the unit has been waterlogged it can be detatched from thge unit and soaked in diesel to free the motor up so it runs again. Once cleaned up and running again attach it back to thge pump unit and reposition the whole unit in the recess on the left side of the trunk behind thge sidewall carpet. There is a bracket behind the carpet that can be used to strap the unit to using tiewraps. Try and position the unit as upright as you can get it ensuring the oil level in it is at the level mark on the side of the reservoir, top up with hydraulic jack oil or get some from BMW. There is a Youtube video that shows how to reposition the unit into the trunk.
https://www.youtube.com/watch?v=NPhwOO654JA
I would guess the shop that quoted you the high price would remove the hood to get at the unit, doubt they would do it through the trunk, hence the high price they want. Hardest part if you do it yourself is breaking the nylon tie wrap that holds the unit in the cavity so you can lift it up and back into the trunk.
Don't forget to rod the drains out and do it on a regular basis, both sides to allow any future build up of water to drain away.