You can approximate missing values using na.approx
for linear/constant approx or na.spline for polynomial one.
## new index to be used
new.index <-
seq(min(index(TS1)),max(index(TS1)), by=as.difftime(10,units='mins'))
## linear approx
TS1.new <- na.approx(merge(TS1 ,xts(NULL,new.index)))
Now you can susbtract your ts, (even if maybe you should check that they have same start dates)
TS2-TS1.new