While I agree there are potential conflicting moves that can cause concern, Thameslink trains don't have to use the up fast heading towards London Bridge, as the down spur is reversible. It would still cause a blockage on the slow lines at Chislehurst, but not as much as if it had to block 3 out of 4 lines. Also they did upgrade the junction by Chislehurst station a few years back to allow 40mph all the way through for train movements on the reversible line, rather than 20mph at the Chislehurst end, possible by removing the diamond crossing and adjusting the entry/exit (this also removed the 60mph restriction in an otherwise 70 zone on both fast and slow lines).
The only concern left as a result is if the Thameslink service were to get stuck behind stopping services on the SEML, although as there's only 4tph through to Hither Green that's less of a concern, then after that it would just avoid Lewisham and any delays into/out of London Bridge would probably be accounted for in the timetable like with other services.