Yes runny pecan pie is safe to eat but not as good as pecan pie that is cooked to perfection.
The runny pecan pie is okay to eat and will do you no harm but the runny pecan pie may not be as good to eat as a non runny pecan pie.
When you have a runny pecan pie it usually means that you didn't add enough ingredients to make the pecan pie solid and not runny.
You can make the pecan pie not runny by adding a fourth egg or a tablespoon of flour or cornstarch to the pie when you make the pecan pie.
Add a bit more of egg, flour or cornstarch than you did previously and then the pecan pie should turn out just right without being runny.