As an alternative solution for Sublime Text (if you want to keep the new OS key mappings) you can add the following lines to your user key bindings file (in menu Subline Text 2 > Preferences > Key Bindings - User):
{ "keys": ["super+shift+up"], "command": "swap_line_up" },
{ "keys": ["super+shift+down"], "command": "swap_line_down" }
This will map ⌘+Shift+↑ or ↓ to the Swap Line Up/Down commands.
A similar issue exists with the batch selection commands usually mapped to Ctrl+Shift+↑ or ↓.
These can be remapped using the following settings:
{ "keys": ["ctrl+alt+shift+up"], "command": "select_lines", "args": {"forward": false} },
{ "keys": ["ctrl+alt+shift+down"], "command": "select_lines", "args": {"forward": true} }
This will map Ctrl+Alt+Shift+↑ or ↓ to the batch selection commands.
Obviously you can change the combinations to whatever you prefer, but these did not seem to be used for anything.