Is it okay to level up skills I don't consider to be my main skills?

Should I avoid overusing skills that I do not plan on spending my perks on? By doing so, will it make it harder for me to reach 100 in the skills that I am planning on spending perks points in? Will I end up too balanced and not a master in anything?

For example I want to get Destruction and Conjuration to 100. If I start raising Smithing - a skill I have not been using at all - my overall char level is going to improve so I won't get the ones I really want before I hit level 50.

Leveling up skills you don't use has no bearing on the skills you do use. They will level up at the same rate no matter what. However, you need to keep in mind that Skyrim uses leveling scaling. So if you pump up a bunch of skills you don't use, like Smithing, and don't level up your main skills to match, you will no doubt run into some serious problems dealing with the higher level enemies.

You also need to consider that the only benefit to leveling up is you get an increase to either magicka, health, or stamina; and gain one additional perk point.

Perk points are useless unless you spend them, and perks have a skill level restriction, so if you only have 30 points into conjuration it doesn't matter how many perks you have, because you won't be able to use most of the perk tree anyways.

So in summary, although it is possible to power level by using skills like smithing, unless you plan to use those skills or are in desperate needs of either some perks or health/stamina/magicka, I would suggest against it. This doesn't mean you shouldn't put points into those skills you don't plan to put perks into, but you should be careful about gaining too many levels by power leveling those perks.

Yes, it's okay to level up other skills. You're limited to 80 perks, so that's what you need to be worried about, not wasting them in areas you're not concerned about.

The level cap does not appear to be 50, rather 81.

Wipqozn's answer is pretty good. I agree with all that.

Here's a fairly simple rule of thumb I use:

Don't level your off-skills unless you've unlocked access to perks in your main skill trees that you need perk points to learn.

So, basically, let's say you use One-Handed swords. You have leveled it up to 60, but only have the first rank of the damage increasing perk. This would be a good time to level some off-skill, like Two-Handed swords, so that you can earn some perk points to increase your damage in One-Handed swords.

Since those levels in Two-Handed swords went toward increasing the damage of One-Handed swords, they won't result in you becoming weaker relative to enemies of your new, higher level.