Getting the glue deep into the existing cracks might be difficult. I've heard of glue injectors that are presumably designed for this problem. Instead of that I was thinking of trying to widen the crack with a lever to get glue in there without an injector
While glue injectors (or often the cheaper alternatives, hypodermics or meat injectors) do work well they're hardly necessary to get glue into a simple crack of the sort seen in the first photo, even when they're much deeper than this.
You can get glue into a crack by any means that gets glue into the crack, including letting gravity do some of the work for you, teasing it in using many different types of long tool1, carrying it in using thread and a very useful method to achieve deep penetration, blowing it in — in a well-equipped workshop compressed air will often be used for this but you can do quite a decent job with a straw, and an even better job using the hollow tube scavenged from a disposable ballpoint (yes I do have a couple of these in my toolkit!)
And yes, it's perfectly fine to lever the crack open a bit to help get the glue where you want. This is virtually standard practice from what I've seen, and except for very tiny surface cracks I'll nearly always do this myself.
If I did break it further would that even be an issue if I was to glue it back together?
No. And in fact during repairs cracks are often extended, to fully separate a cracked board.
The main reason is not to make glue application easier, but to clean the surfaces. As mentioned in some previous Answers (example) only clean/dust-free, freshly exposed, wood actually glues together at maximum strength. Old cracks2, even if they are not visibly dirty or dusty, won't glue together as strongly as they could but sometimes you have no choice except to get glue into the crack, clamp the crack closed and hope for the best.
While the spider web (?) at the end of the second crack seems to show this could do with some careful cleaning I would not further separate it because it's an interrupted split, rather than a classic v-shaped simple crack that follows a grain line. You're going to have to do what you can here to clean the open end and then get glue into every portion of the cracking. Injecting the glue in would certainly help with portions of this crack.
Second question: The pin holes are going to get full of glue when I go this. I'm okay making the pins permanent features here so was going to insert them during the gluing process. The alternative would be to drill the glue out of the holes afterwards.
Glueing the dowels in is actually one way of making the bench more sturdy, so it's well worth doing anyway — many experienced assemblers of Ikea and similar furniture will glue some or all of the dowels even when the instructions don't specify, to add to the strength of the piece.
Any other thoughts on how to preserver holes when gluing something like this?
If the dowels were intended not to be glued in waxing them thoroughly and inserting them during the glue-up will work well, and is actually preferable to drilling the holes out afterwards3. Wax is a universal glue resister and very useful where you don't want glue to penetrate a surface, or accidentally bond two things together.
A note on clamping
As mentioned in the link included above, don't be shy about clamping the piece back together very tightly. You can't overclamp as far as the glue joint is concerned. It doesn't matter how much glue squeezes out because you can't starve the joint, if you applied enough glue to begin with such that it fully wetted both surfaces.
1 Sewing needles, an awl or icepick, screwdriver tip, coffee stirrer, bamboo skewer, toothpick, the list goes on and on :-)
2 You don't have to be super fussy about this, but 'old' here should be understood to be anything older than a few hours. Not days, hours. In a perfect world cracks would be glued within minutes of them happening, where strength is important.
3 Because doing this will likely wallow out the holes. Even taking a thou or two off the inside of the dowel holes, making them a slightly looser fit, is enough to compromise strength somewhat. Unglued dowels should never be a loose fit in their holes, they should be an 'interference fit' or tighter, requiring somewhere between significant finger pressure and light taps from a hammer or mallet to get them fully seated.