Sorry she is having a hard time with it!!
I do feel for both of you, it's not fun to have a hard time in gym.
My dd struggles with strength/conditioning as well, but for her it's the upper body/core. I'm not concerned in any way that there is a physical problem, just something she struggles with and doesn't like because it is very hard for her. She's built more compact than the ideal gymnast (not heavy at all, just not super skinny/strong).
To "help" her I sometimes point out specific tricks she would like to learn someday and explain exactly how much core or upper body strength the move will require, more than what she now. She knows it's a must for her to do it, but she definitely does NOT like it. There will likely come a time in a few years where she will have to repeat or stall completely because of bars unless she amps up her strength drastically (no, she is not aware of this at all yet, I would certainly not tell her at this point).
To be fair, my dd may actually cry during some especially grueling conditioning pass BUT she won't whine about it neither to her coaches nor to me.
She's 9, currently a L4 and we are hoping she will compete L5 next year.
If it were my dd, I would calmly discuss it with her (again?), and let her know how necessary it is. Point to specific tricks with lots of leg power involved. Make sure there isn't an actual physical reason why it's more difficult for her than other girls.... And then tell her to suck it up and do it if she wants to progress. I know it may not be a popular opinion but in lots of sports, this being one of them, there's a certain amount of "suck it up buttercup" involved. I tell it to my gymmie when her muscles are sore or she has rips. I tell it to my ballerina when her feet are blistered and bruised. If there is no injury, "just" normal soreness from the activity they have chosen. They both have the tools to help themselves and I will gladly help, but I won't listen to whining about it if it's a normal part of their passion. Sorry, off on a tangent there, could be because gymmie has been a little whiny about her hands as they are working lots of BHS on beam...
As far as "sneaky" leg conditioning, ice skating and roller skating is great. Go for runs and bike rides together. Legs seem to me that they would probably be one of the easier ones to incorporate into fun activities that she wouldn't even realize is targeted towards her getting stronger... Best of luck!!!