OD shouldn't be checking runes anyway, he isn't really an early game ganker, it works best if there is a roamer or somebody in the sidelanes checking for runes and utilizing them. You should get one level of arcane orb after your banish and passive, but then not again until those are maxed and you have a level in your ult. It simply costs too much mana and isn't all that great until your passive and mana pool can keep up. For squishyness you should invest into a rod of atos; its pretty much designed for OD and Silencer. With an atos/force/treads OD can easily be active with his team as well as farm up the rest of his items fast.
Against an SF mid you should be banishing him as much as possible because he won't be able to use razes, if you can time them in order to deny him xp and gold, thats great, but just stealing int from an SF can screw them over.