Well, she can't protect herself unless she activates John's Pen, her magic's sealed, her Walking Church is broken, the Science Side doesn't really care about her, no Esper can use magic, Komoe isn't wanting magic lessons and has teacher stuff.
And, any non-Kamijou-Faction mage would want to steal her. And she doesn't like her John's Pen mode, so putting herself in danger to activate it, like In Memoriam seems to be a last resort option.
Lastly, I guess? Academy City is the direct opposite of the Magic Side, so there usually aren't many mages to fight? If there are, Tsumichikado goes to Touma instead of Index, Touma leaves Index alone to not drag herself into things. Her Mana Radar doesn't seem to work over the whole city, so she can't tell when a mage enters the city and respond ASAP.