If we, or rather I, admitted that Madeleine had died in an accident in the apartment, and confessed to having hidden and disposed of her body, the sentence I’d receive would be much more lenient: only two years, he said, as
opposed to what I’d be looking at if I ended up being charged with homicide......The incentive to accept this ‘offer’ seemed to be that if we didn’t agree to it, the authorities could or would go after us for murder, and if we were found guilty, we might both receive life sentences. Was this what it came down to? Confess to this lesser charge
or risk something much worse? [Madeleine]
Leaving the idea of a 'deal' aside, Kate's lawyer seems to warning her what could happen, which was his job. If they were involved their best move at that moment would have been to own up and for Kate to serve a short sentence. If they didn't do that and were eventually charged, tried and found guilty of murder the consequences would be much greater.
If Kate heard two and two and made five instead of four it's understandable. The fact remains the files contain no evidence to suggest that the parents were suspected of murder. Even Harrison's brief from Encarnacao can't be seen as due to suspicion of the parents. We don't know why Encarnacao used that word.