You mention that you have both created the company so his contribution did have some value; you even say you've contributed about half the effort each so 50% seems fair, at the moment.
However, you're limiting your thinking by assuming there will always be a fixed amount of shares and that 50/50 now is 50/50 forever.
Let's say you incorporate and each get 100,000 shares (I'll continue using this figure for this example), with no outside partners: you both effectively own 50% of the company. Let's say that you draft a stock option plan for employees and allocate 50,000 shares: now you each own 40% of the company. And so ownership changes as the business grows because the number of outstanding shares evolve.
Now, how can you solve your issue? By both agreeing that you should receive stock options that vest over time. For instance, you could issue a warrant for 48,000 shares that vests over 4 years: each month you work there, you earn an additional 1,000 shares. And then he could also have such plan so that if/when he comes back, he also earns 1,000 per month. Or something like that.
What's important with partners is that each has a share of the company that makes sense relative to the share of the other. So when an investor comes in and funds you with 1Mio, he might also get 100,000 shares. Now the cap table will be 100K for you, 100K for your partner, 100K for the investor, 50K for the employees; 350K shares total (plus your vesting warrants) and even thought neither of you owns 50% of the company, both of you are happy because you own a similar stake. And since you're working there, you keep accumulating shares with the vesting of the warrant.