The problem that might come up when you baste with thread (whether by hand or machine) before machine quilting is that you might have trouble removing the basting stitches, particularly if the machine quilting needle happens to pierce the basting thread (which will happen more often than you would think). You can remove the basting thread as you go, but depending on the type of quilting design you're doing, that might either slow you down or loosen up the quilt sandwich. I guess that's where pin basting has an advantage (and like you I hated pin basting). You can also baste using water soluble thread, although I have only done that when machine basting and don't know how well that thread would perform when hand basting.