In Tzolk'in, can you be at negative points?
Yes.  This is explicitly stated on page 13 of the rules.


  "On each temple, you score the number of victory points indicated by your current step only. Note that if you are on the bottom step, you will lose vic- tory points. Victory points can go negative."


However it appears from your question you are scoring the -1 when you move onto that space.  This is incorrect as you only score points on the temples during the mid game and endgame food days.