For the taxi back, get the Addison Lee app on a smartphone and book through that. Addison Lee are the biggest 'private' taxi company in London and will be a bit cheaper than a black cab. It should cost about £25. You're only going from E to SE London - it's only about 10 minutes drive.
In terms of walking, it's not really convenient. The area around Excel is actually quite nice and not 'dodgy' at all. However,the DLR line just north of it separates the 'quite nice' area from the 'dodginess' of Canning Town. As far as Greenwich goes, North Greenwich can be quite dodgy but Greenwich itself is really ultra nice. The Greenwich Travelodge is located in Deptford Bridge I think, which is a short walk from Greenwich. Deptford itself is a bit grim and I wouldn't walk there at night. Deptford Bridge is mainly composed of newly built highrise flats and is quite nice. I think the Travelodge is nesstled within the newbuilds. I wouldn't really recommend walking from there to Greenwich though as the road you'd want to go down (Blackheath Road) isn't particularly well lit and at the place where it turns into Blackheath Hill, there is quite a bit of social housing (that's all due to be knocked down and redeveloped). Greenwich and the areas around it is typical of the whole London feel where there are really nice places next to not so nice places. Walk up to Greenwich and Blackheath and there are big houses that cost in the millions!
If you've got some time to spend around Greenwich, go check out the market on the weekend - especially the Chinese takeaway stall if it's there. The only problem with Greenwich is that it can get a bit 'touristy'. Have a walk over the heath to Blackheath Village, it's really nice there too. In Greenwich, check out the Greenwich Union pub - absolutely brilliant place.
FYI I used to live just south of the dock near to the Excel but moved to between Blackheath and Greenwich about six months ago so I know both areas pretty well!! :)
If you're concerned about parking, one idea might be to park in North Greenwich near the O2 and use the cable car to get over the river. This does depend on the hours you're thinking of going though as the cable car does stop running earlier than the tube.