"my thoughts are with you."

No!! No we don't.
Prayer is simply the the single most vainglorious and self aggrandizing way of doing fuck all.
As an atheist I do not require a secular equivalent for that.

We do not need thoughts and prayers. We need action.

Think of actions, not words.

Parkland didn't have anything to do with that. It's always been meaningless. The non-religious version is "Sucks to be you." Both phrases mean the same thing.

How can I help?

Sending good vibes and positive energy..

Condolences first, assistance if feasible... “thoughts and prayers” was no a terrible thing to say other than “we” being off the religious bit... problem is only that it became a hollow automatic response from people who obviously couldn’t give two shits, and they are the very people in positions and with the power to offer real needed assistance, which was not forthcoming due to greed, prejudice and hate... poorly disguised as giving a shit.

"I'm sorry for your loss. What can I do to help?"

That's not quite it, but I agree, it's hard to come up with something that conveys the right meaning, but is still concise enough to use.