Yes it can, and it would be fairly easy if water has not made it back to the reservoir. If water has made it back to the reservoir, I would pull it and clean the reservoir before flushing the system. It is really easy and might take all of 30 minutes from start to finish. If you have to take the pump apart, do NOT take the valve control body off of the bottom of the pump. You will have to replace 4 o-rings inside there if you do.
Otherwise to flush the lines:
I would usually tell you to start with the rams in the down position, however if you sucked water into the rams when you manually lifted it, I would not advise that. Lowering the rams with the hoses connected using the trim pump would force any water in the rams back through the system and into the reservoir. Just by undoing the up lines, the rams should lower themselves. Make sure you have a bin underneath the system to catch the oil. Disconnect the up lines and run the system "up" and watch for clean oil to come out. Repeat with the down system.
Here is a link to the hydraulic schematic on an MC-1:
http://boatinfo.no/lib/mercruiser/manuals/mercruiser4.html#/134
Read through the entire section to see what you are dealing with before you start. Bleeding procedures are in there is well if you have to take the rams apart.
If you think there is water in the rams, take them off and disassemble them, clean them out, re-assemble, and bleed the system. This is really easy on the MC-1 system. The first ram might take you 45 minutes as you are learning it, but the 2nd one should take you under 20. It will be a never-ending cycle to get the water out of the rams without taking them apart.
IMHO, there has to be a reason that hose popped off. You need to diagnose that. Possibly stripped threads on the housing of the ram? You can buy just that housing for relatively cheap. Mercruiser # 77442A1
While you have it apart, you can change the seals as well. The whole kit is just a bunch of o-rings. Merc 25-60342A2
I have torn my entire system apart this summer and re-built it. If you have any questions, just ask.