I hate i when this happens! If you have a decapping die, disassemble the priming tool, take the case with the cocked primer, and the priming tool shellholder, on over to your press, and set them on the ram. Gently raise the ram until the decapping rod protrudes through the flash hole. Gently press the cocked primer out.
I have never had one detonate doing this, but there is always that risk, so plan accordingly and use appropriate safety gear including safety glasses.
ETA: Not a dig at Lee. I love the feel their hand priming tool delivers. But I got tired of cocked primers, and upside down primers, and the lid popping off, so I bought the RCBS APS hand primer tool, and I must say I have had none of these issues since. I did have some issues initially, but once the bugs were worked out, I have been very happy with that tool. You might consider getting one of them.