Helper function to find rotation of Caesar Cipher
First off, you should follow PEP8.
This will make your code more readable for Python programmers, and there is quite a few tips in there to make your code more Pythonic.
The amount of whitespace that you use is actually pretty good! It's mostly your names that 'let you down'.
But you're following a convention of camelCase. Which is also ok, but snake_case is preferred.

I don't like the re-definition of letterFreq and lines on ever function call.
This leads to a performance hindrance.
And so I'd move them out of the function to make them global.
Also as they are constants you may want to follow PEP8 and name them LETTER_FREQ and WORDS.

After this I'd look into removing the recursion. In Python recursion is cute, and un-reliable, nothing more.
I'd recommend that you don't use it, and instead you can use a for loop.
Using range starting at iterator and ending at len(LETTER_FREQ) we can remove the need for the recursion.

I'd also remove the print, instead of calling it in the function you should do it outside of the function.
If I'm using this function I don't want a print there ever couple of minutes.

Finally your turnery is a bit awkward and so I'd change it to use the modulo function, %.
This allows you to remove the if/else as -1 % 26 == 25 and so we can replace it with chr((ord(letter) - rot - 65) % 26 + 65).

Adding all the above together lead me to:

LETTER_FREQ = "AEIOTU"

with open('words.txt', 'r') as f:
    WORDS = [word.upper().strip() for word in f.readlines()]

def find_rotation(word1, word2, iterator=0):
    for index in range(iterator, len(LETTER_FREQ)):
        rot = ord(word1) - ord(LETTER_FREQ[index])
        letters = ''.join([chr((ord(letter) - rot - 65) % 26 + 65) for letter in word2])
        if letters in WORDS:
            return rot
    return None




For an additional speed you can also change WORDS to be a set, WORDS = set(WORDS), this is as it'll then be \$O(1)\$ look up in the if letters in WORDS: line, rather than \$O(n)\$. This is good as if the words list is large then it'll take a significantly larger amount of time then it would with a set.