Rasputin is a being of logic, according to his calculations he couldn't afford to let the Traveller leave. The info in the alpha lupi grimoire is probably for the player, Rapsutin didn't know she planned to stay he simply went for the most effective course of action. By keeping the Traveller here Rasputin gave us a higher purpose, not only are we fighting for our homeworld but also for the last hope of the light.