You have broken your contract, for which yiu may receive a warning... but that should be all.. ask ACAS for advice as to whether they can prevent you from having this secind job, whether you can present evidence that they ignore other people in the same position therefore the warning is unfair and also ask them if it is worth also presenting the other discrimination evidence at this meeting.
Pregnancy discrimination: have a seperate discussion about this, either with Pregnant them Skrewed or ACAS or both... you might want to bring a grievance if you can see a possible resolution.
Being paid to do your partner's invoicing: of course you should not do this without being paid. It is a common scenario for self employed people who's partners help. It is also a common way of reducing the amount of tax paid by the company and your partner, overall.
The company has profits of £100k.. pays your partner £50k (up to 20% tax band) and is taxed on the £50k profit.. if you receive £10K.. tax is only on £40k. What matters is how much tax is paid.. and will depend if your marginal tax rate is lower.. which is likely given what you have explained.
Where you have 2 jobs, you decide which job uses your tax free allowance - £12.6k ... you can not claim it twice. If you earn enough in your first job to use up the £12.6k, you will be taxed in your second job at 20% unless your total earnings are above £50k in which case, some will be taxed at 45%.
You should have your partners accountant explain this to you as it affects your tax as well as your net pay.
Also worth noting that your partner could pay for your expenses while on maternity leave, out of his taxed pay, or he could pay you now, at a lower tax rate, reducing his overall taxes.. and save himself money overall.. it is a smart tax move.. but you do need to understand the impact on your taxes and also see this as a joint family decision from a company you both work for... it is not soley generosity on his part.. even if it makes financial sense.