I think
@kamikaze made a really good point about pain - whilst I know it's probably because your pup doesn't like being disturbed - if this extends to all handling she could be in pain. Best to rule that out I believe.
I think people may be being a little harsh. Your goal is not to cause emotional distress to your dog, it is to develop a working relationship in which you can live in harmony with her. Unfortunately the advice you have read on here is unlikely to lead you to that goal. That's not your fault and you're not an awful person for considering that. There are many people who seek help training their dog - because they care and they want to support their development and breed a successful relationship in which all members of the family are happy and secure. Again, unfortunately there are a lot of 'professional' dog trainers who will buy so heavily into the dominance theory - often incorrectly (not refuting the theory, moreso the ways in which behaviours are addressed under these assumptions).
Not to go into this too much, but if we consider the dominance theory and the idea that dogs form packs with the goal of rising the ranks - not an approach I am suggesting to use but just using it hypothetically to explore the longer conseqeunces and learning. So THIS THEORY would suggest that techniques to address so called dominance behaviours - such as holding down, the dog learns to be 'submissive' to you. But when he also learns is that 'dominance' is maintained by physical force. So as the underpinnings of the theory suggests, your dog may want to one day rise the chain so the way they've learnt to do this is through physical force, because the control fear environment has been established. As prior to editing some people got confused by this: to confirm I am not promoting, endorsing or condoning this approach, merely pointing out one of the many flaws in its theoretical and practical basis. And in case this is still confusing - I'm saying don't hold your dog down because I don't think it will work or be nice for either you or your dog.
If you're just picking your pup up because you want some cuddles, that's lovely, but probably not helpful. There will be times when you need to move your pup when she is sleeping. It's impossible to rule that out completely.
As mentioned, you may want to wake her vocally, call her over for a treat or a toy (whether she is food or play driven - doesn't sound like she's affection driven!). You do need to get her used to being handled because if god forbid she is in pain, or ever is in future, the vet will need to be able to give her a thorough inspection and if she doesn't like being handled - this will likely be extremely traumatic. Get her used to you touching her - pair it with praise and treats. Start really really slowly. If she growls, you've gone too fast. So go back to the step before and give her lots of treats and attention.
You seem really committed to helping your pup. It may be really useful for you to remember that positive reinforcement and praise is not only nicer for you and your dog, but it also builds stronger associations - thus pups learn quicker this way. Sure the prong collars and choke chains work - but slower, less humanely and only when they are present - the dog doesn't learn what to do through their own volition so as soon as the punishment is gone, they will regress. This is not just my opinion, it's consistently demonstrated in behavioural psychology literature.
Hope this helps and all the best with your pup
