Well, sorry but it does seem a bit facile - plus earthquakes DO occur naturally. Wouldn't it be more interesting to focus on the consequences and aftermath of the earthquake rather than its causes or trying to find a "secret" cause involving aliens and such?
Especially since the aftermath of the Lisbon earthquake were were quite horrendous (auto-da-fés, religious persecutions etc.) - as mentioned in Voltaire's "Candide".
Imagine a group of time travellers arriving right after the earthquake; it would not take long for them to be arrested as "sorcerers" or "heretics / miscreants" whose actions and "impious" behavior would be held responsible for the "wrath of god" (i.e. the earthquake).
This disaster marked the end of Portugal's role as one of the major powers in Europe; it also had crucial cultural, political, theological and philosophical consequences. In other words, it was a history-changing event, with many fascinating repercussions - in other words, prime material for a classic Hartnell-like historical episode!
On the other hand, if you really want to inject some "alien element" in this event, an earthquake of such magnitude might also have the accidental unearthing / awakening of a Silurian colony - and imagine what would happen when reptilian "demons" are seen by faith-blinded survivors of the earthquake...
I like the idea of dropping the party in for the aftermath, though a little beforehand is (IMO) batter as they'll probably try and save people, thus worsening things for themselves (obviously they're witches/sorcerers).
The main reasons for the extreme devastation are (excluding aliens et cetera) are threefold:
It was an immensely energetic event, over 8.0 on the MM scale (some put it at 9.0, probably the most powerful in recorded history)
Lisbon was utterly unprepared for the event, buildings weren't constructed to withstand such energies, and the city was densely packed.
The seismic event occurred at sea, creating a devastating tsunami.
The event caused serious damage in North Africa (along with at least ten thousand deaths) and effected Britain and Ireland (damaging Galway and creating Aughinish Island) along with the east coast of South America.
If you're going to have it caused by (say) a spaceship crash then explorations of the seabed near Cape St. Vincent might lead to some interesting finds, beyond U-93.
Time, time,time, see what’s become of me. While I looked around for my possibilities... My AITAS files.