I’m sure I read years ago about how the glowing eyes were added to the end of MI2 to provide an out if needed, so I personally have always disregarded that detail and taken the rest of the ending for what it is.
When looked at that way, the whole ending chapter is fairly literal and easy to understand. It’s two kids messing around, supported by numerous clues throughout the first two games. What else could it mean?
The ambiguity always came from the glowing eyes at the end, but that has been cleared up by interviews and Return (including its little ending note).