I walk round there most days...
Normally - as you know - you'd walk along the river (past the mayor's office) then up the steps onto Tower Bridge, and over the bridge. However, with the Marathon, Lord knows where the crossings will be. As you say, there's a tunnel under the road at Tower Hill, so you can double back on yourself from the bridge, which solves the problem as long as Minories isn't closed...
If you're keen to DLR, I'd be tempted to walk from London Bridge up to Bank and start the DLR from there, or at least walk over London Bridge and wiggle round to Tower Hill on the north side of the river