Yeah
, I had exactly the same experience, i played 1.09 before and it was a breeze at DIF 6 - suddenly the patch came and about 400 teleport stations appeared next to my human settlement, within 1 second i was 220 progress points up and one less planet to go, what before was a stable situation now as a slugfest with multi 1k fleets incoming (my progression was 600+ then ,p)
The patches for this game bring about immense changes - Nice formational movement - Even more formidable AI and all my favorite AI exploits fixed ;/
Now i have always at least 1 starship and 100 ships in a sector and LOTS of tractor turrets (if you want to protect your command station you can plant tractor turrets midway between wormhole and command station to give you some more time to respond. Usually the ai will go for harvesters anyway - giving you even more time to put tractors down. Found these things are great helpers anywhere, now i have at least 15 next to each wormhole and always at least 10 of those under a shield. But that still only protects against 65-100 ships
With 600 ships i'd be shocked as well - if you are really worried about defending this, use lightning missiles on that fleet (helps to always have at least one in any of your sectors).
Generally, the price of 1 lightning missile is always better to pay than loosing your command station
(much less progression too).But to quote X "The Score is a very misleading factor" as i had to experience myself after the patches many times.