I had the same problems and solved it by remuxing and changing the frame rate to half. This can be done using tsMuxer, which has a command line interface. Downside is it can not output in MOV format, but in m2ts or ts. I wrote a simple python script to find all MOV files in the current directory, generate the input file to tsMuxer with framerate according to input and run it. Probably exists better ways, but this is one way.
import os
import sys
allFilesAndFolders = os.listdir(".")
cwd = os.getcwd()
fps = sys.argv[1]
filename = "Slower.META"
for entry in allFilesAndFolders:
if entry.endswith(".MOV"):
if os.path.isfile(filename):
os.remove(filename)
with open(filename, "a+") as myFile:
myFile.write("MUXOPT --no-pcr-on-video-pid --new-audio-pes --vbr --vbv-len=500\n")
myFile.write("V_MPEG4/ISO/AVC, \"" + cwd + "\\" + entry + "\", fps=" + fps + ", insertSEI, contSPS, ar=As source, track=1\n")
os.system("\"C:\Program Files (x86)\\tsMuxeR_2.6.12\\tsMuxeR.exe\" " + filename + " " + entry.split(".")[0] + "_slow.m2ts")