You are catrasophising something that hasn't even happened yet, so stop and take a breath.
Firstly, you need to decide when to tell them you're pregnant. You don't have to do this straight away. You can wait until you start showing or even your 20 week scan. If from that point you believe you are being treated differently because of your pregnancy, start making a diary of evidence and speak to HR.
Whilst HR may be perceived by the employee as working for the employer, most HR personnel advocate and mediate constantly between management and employees, and ultimately their professionalism would be brought into question if they ignore blatant discrimination.
Secondly, why are you worrying about your job and something that may or may not happen in potentially 12+ months time (assuming you are 3 months now)? Businesses change, people change, who knows you might even change, and want to return full time...
Take stock in the fact that you are legally protected whilst pregnant.
Employers shouldn't be asking your plans after you've had the baby, so if they ask (they shouldn't) reply with a blanket answer of "I haven't decided what I'm doing yet, I have 9 months to decide".
Request the flexible working policy closer to your leave date and when you know where your at after your baby, you can decide from there.
Congratulations by the way.