Eagle - How to make the router ignore internally connected pins (in a package)

In eagle 7 your problem is solved. klick on the symbol in the connect-dialog (red cyrcle), so you can change if the pins of the same signal have to be connected in the layout.

The important part of the answer is yes, but for what it seems you're actually interested in the answer is no.

Eagle is treating them as connected internally for the design rule checks (DRC). But that doesn't mean the autorouter can be smart about it.

In Eagle 6 you can define connections the way you have in your part; you only need to create one pin to connect to multiple pads, as Cadsoft puts it:

You can now connect one pin in the schematic symbol to any number of pads of the package. With this function EAGLE can handle components internal connected pins. Compared to previous versions schematic symbols look nicer and you save time in defining them.

The autorouter is not that clever though. Its default behavior actually makes sense too, if at all possible, pads should be connected externally as well. It takes a human to see the 'cleaner' way. With a bit of thought on the plethora of additional combinations the autorouter would have if it opened the option of not externally connecting internally connected pads it makes sense why Cadsoft left it out.

The modification you made to what the autorouter did is not a violation because Eagle recognizes those pads as internally connected. You could, in fact, connect only half the pads (not any half) without error.

You'll often need to clean up after the autorouter, at least in this case you don't need to waive any DRCs.